HEADER RIBONUCLEIC ACID 11-MAY-01 TITLE HIGH RESOLUTION NEUTRON STRUCTURE OF NICOTINAMIDE ADENINE TITLE 2 DINUCLEOTIDE (NAD+) COMPND NULL SOURCE NULL KEYWDS NAD+, NEUTRON, ACIDIC EXPDTA NEUTRON DIFFRACTION AUTHOR B.GUILLOT,C.LECOMTE,A.COUSSON,C.SCHERF,C.JELSCH REVDAT 1 22-JUN-01 0 JRNL AUTH B.GUILLOT,C.LECOMTE,A.COUSSON,C.SCHERF,C.JELSCH JRNL TITL HIGH RESOLUTION NEUTRON STRUCTURE OF NICOTINAMIDE JRNL TITL 2 ADENINE DINUCLEOTIDE JRNL REF ACTA CRYSTALLOGR., SECT.D V. 57 981 2001 JRNL REFN ASTM ABCRE6 DK ISSN 0907-4449 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 0.65 ANGSTROM. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : MOPRO REMARK 3 AUTHORS : GUILLOT,VIRY,GUILLOT,LECOMTE,JELSCH REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 11.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.0 REMARK 3 NUMBER OF REFLECTIONS : 4988 REMARK 3 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.062 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 0 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 0.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 0.68 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 41.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 268 REMARK 3 BIN R VALUE (WORKING SET) : 0.0800 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 71 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 0.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 1.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DATA CUTOFF (SIGMA(I) IS 3.000, REMARK 3 R VALUE (ALL REFLECTIONS) IS 0.095, HIGHEST RESOLUTION REMARK 3 BIN R VALUE (ALL REFLECTIONS) IS 0.160, ESTIMATED REMARK 3 COORDINATE ERROR BY NORMAL MATRIX INVERSION (A) IS 0.0012 REMARK 4 REMARK 4 NULL COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY THE NUCLEIC ACID DATABASE REMARK 100 ON 15-MAY-2001. REMARK 100 THE NDB ID CODE IS UR0013. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 21-MAR-2000 REMARK 230 TEMPERATURE (KELVIN) : 100.0 REMARK 230 PH : 3.50 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : 5C2 REMARK 230 WAVELENGTH OR RANGE (A) : 0.8305 REMARK 230 MONOCHROMATOR : CU(220) REMARK 230 OPTICS : MONOCHROMATOR REMARK 230 REMARK 230 DETECTOR TYPE : DIFFRACTOMETER REMARK 230 DETECTOR MANUFACTURER : STOE FOUR CIRCLES REMARK 230 INTENSITY-INTEGRATION SOFTWARE : DIF4N REMARK 230 DATA SCALING SOFTWARE : PRON REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 5990 REMARK 230 RESOLUTION RANGE HIGH (A) : 0.650 REMARK 230 RESOLUTION RANGE LOW (A) : 11.200 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 230 DATA REDUNDANCY : 1.060 REMARK 230 R MERGE (I) : 0.05600 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 12.9000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.65 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.67 REMARK 230 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 230 DATA REDUNDANCY IN SHELL : 1.00 REMARK 230 R MERGE FOR SHELL (I) : NULL REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 6.500 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 230 SOFTWARE USED :SHELXS REMARK 230 STARTING MODEL: NULL REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 15.0 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: METHANOL, LIOH REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF NULLCHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 HET NAJ 1 71 HETNAM NAJ NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) FORMUL 1 NAJ C21 H27 N7 O14 P2 FORMUL 2 HOH *4(H2 O1) CRYST1 8.576 8.829 11.191 109.70 90.60 104.06 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.116604 0.029194 0.012219 0.00000 SCALE2 0.000000 0.116766 0.043639 0.00000 SCALE3 0.000000 0.000000 0.095399 0.00000 HETATM 1 AP NAJ 1 3.124 -3.638 1.598 1.00 0.59 P HETATM 2 AO1 NAJ 1 3.694 -2.694 0.579 1.00 0.85 O HETATM 3 AO2 NAJ 1 2.995 -5.050 1.152 1.00 0.98 O HETATM 4 AO5* NAJ 1 3.968 -3.551 2.951 1.00 0.83 O HETATM 5 AC5* NAJ 1 5.349 -3.986 2.860 1.00 0.81 C HETATM 6 AC4* NAJ 1 5.758 -4.610 4.167 1.00 0.60 C HETATM 7 AO4* NAJ 1 5.732 -3.615 5.215 1.00 0.81 O HETATM 8 AC3* NAJ 1 4.879 -5.748 4.668 1.00 0.56 C HETATM 9 AO3* NAJ 1 5.710 -6.625 5.419 1.00 0.86 O HETATM 10 AC2* NAJ 1 3.877 -5.025 5.584 1.00 0.61 C HETATM 11 AO2* NAJ 1 3.309 -5.856 6.551 1.00 0.94 O HETATM 12 AC1* NAJ 1 4.764 -3.908 6.179 1.00 0.60 C HETATM 13 AN9 NAJ 1 4.031 -2.683 6.472 1.00 0.70 N HETATM 14 AC8 NAJ 1 3.731 -1.682 5.585 1.00 0.75 C HETATM 15 AN7 NAJ 1 3.061 -0.686 6.144 1.00 0.75 N HETATM 16 AC5 NAJ 1 2.915 -1.068 7.454 1.00 0.70 C HETATM 17 AC6 NAJ 1 2.285 -0.424 8.545 1.00 0.65 C HETATM 18 AN6 NAJ 1 1.673 0.738 8.515 1.00 0.93 N HETATM 19 AN1 NAJ 1 2.332 -1.146 9.706 1.00 0.84 N HETATM 20 AC2 NAJ 1 2.988 -2.323 9.834 1.00 0.91 C HETATM 21 AN3 NAJ 1 3.615 -2.944 8.859 1.00 0.92 N HETATM 22 AC4 NAJ 1 3.527 -2.296 7.678 1.00 0.71 C HETATM 23 O3 NAJ 1 1.750 -3.020 2.075 1.00 0.71 O HETATM 24 NP NAJ 1 0.472 -3.673 2.828 1.00 0.60 P HETATM 25 NO1 NAJ 1 0.929 -4.529 3.940 1.00 0.95 O HETATM 26 NO2 NAJ 1 -0.450 -4.213 1.797 1.00 0.84 O HETATM 27 NO5* NAJ 1 -0.190 -2.329 3.380 1.00 0.71 O HETATM 28 NC5* NAJ 1 0.512 -1.671 4.445 1.00 1.04 C HETATM 29 NC4* NAJ 1 -0.115 -0.318 4.664 1.00 0.74 C HETATM 30 NO4* NAJ 1 0.202 0.544 3.537 1.00 0.99 O HETATM 31 NC3* NAJ 1 -1.646 -0.353 4.781 1.00 0.71 C HETATM 32 NO3* NAJ 1 -2.140 0.607 5.689 1.00 1.06 O HETATM 33 NC2* NAJ 1 -2.105 0.071 3.383 1.00 0.73 C HETATM 34 NO2* NAJ 1 -3.368 0.713 3.363 1.00 1.17 O HETATM 35 NC1* NAJ 1 -0.955 0.978 2.919 1.00 0.65 C HETATM 36 NN1 NAJ 1 -0.754 0.900 1.439 1.00 0.66 N HETATM 37 NC2 NAJ 1 -1.427 1.789 0.685 1.00 0.77 C HETATM 38 NC3 NAJ 1 -1.290 1.793 -0.699 1.00 0.77 C HETATM 39 NC7 NAJ 1 -1.939 2.833 -1.564 1.00 0.94 C HETATM 40 NO7 NAJ 1 -1.907 2.691 -2.788 1.00 1.50 O HETATM 41 NN7 NAJ 1 -2.531 3.872 -0.969 1.00 1.25 N HETATM 42 NC4 NAJ 1 -0.448 0.840 -1.281 1.00 0.96 C HETATM 43 NC5 NAJ 1 0.221 -0.066 -0.477 1.00 1.07 C HETATM 44 NC6 NAJ 1 0.073 -0.014 0.893 1.00 0.97 C HETATM 45 AH51 NAJ 1 5.976 -3.137 2.626 1.00 2.30 H HETATM 46 AH52 NAJ 1 5.479 -4.718 2.067 1.00 2.25 H HETATM 47 AH4* NAJ 1 6.786 -4.964 4.051 1.00 1.71 H HETATM 48 AH3* NAJ 1 4.368 -6.290 3.859 1.00 1.85 H HETATM 49 AHO3 NAJ 1 5.265 -7.523 5.559 1.00 1.85 H HETATM 50 AH2* NAJ 1 3.095 -4.575 4.939 1.00 1.43 H HETATM 51 AHO2 NAJ 1 2.370 -5.588 6.668 1.00 1.62 H HETATM 52 AH1* NAJ 1 5.204 -4.252 7.141 1.00 1.82 H HETATM 53 AH8 NAJ 1 4.009 -1.750 4.539 1.00 2.13 H HETATM 54 AH61 NAJ 1 1.420 1.191 9.417 1.00 1.94 H HETATM 55 AH62 NAJ 1 1.670 1.311 7.662 1.00 1.72 H HETATM 56 AH2 NAJ 1 2.962 -2.775 10.838 1.00 2.02 H HETATM 57 AH1 NAJ 1 1.709 -0.809 10.547 1.00 1.73 H HETATM 58 NH51 NAJ 1 1.551 -1.528 4.151 1.00 2.39 H HETATM 59 NH52 NAJ 1 0.453 -2.243 5.357 1.00 2.43 H HETATM 60 NH4* NAJ 1 0.315 0.150 5.571 1.00 1.84 H HETATM 61 NH3* NAJ 1 -1.982 -1.362 5.037 1.00 1.93 H HETATM 62 NHO3 NAJ 1 -2.194 0.138 6.555 1.00 2.01 H HETATM 63 NH2* NAJ 1 -2.157 -0.812 2.721 1.00 1.82 H HETATM 64 NHO2 NAJ 1 -3.502 1.116 4.254 1.00 2.19 H HETATM 65 NH1* NAJ 1 -1.169 2.044 3.135 1.00 1.97 H HETATM 66 NH2 NAJ 1 -2.031 2.509 1.211 1.00 1.83 H HETATM 67 NH71 NAJ 1 -2.905 4.627 -1.573 1.00 2.05 H HETATM 68 NH72 NAJ 1 -2.482 4.042 0.047 1.00 2.34 H HETATM 69 NH4 NAJ 1 -0.310 0.838 -2.376 1.00 2.47 H HETATM 70 NH5 NAJ 1 0.894 -0.808 -0.909 1.00 2.61 H HETATM 71 NH6 NAJ 1 0.590 -0.668 1.597 1.00 2.37 H HETATM 72 O HOH 2 5.619 -1.135 -0.696 1.00 1.34 O HETATM 73 1H HOH 2 5.067 -1.737 -0.162 1.00 2.16 H HETATM 74 2H HOH 2 4.993 -0.473 -1.022 1.00 2.47 H HETATM 75 O HOH 3 -1.427 -6.304 7.886 1.00 1.32 O HETATM 76 1H HOH 3 -2.027 -5.853 8.505 1.00 2.12 H HETATM 77 2H HOH 3 -1.933 -6.411 7.036 1.00 2.58 H HETATM 78 O HOH 4 0.813 -4.851 6.663 1.00 1.14 O HETATM 79 1H HOH 4 0.100 -5.411 6.986 1.00 2.39 H HETATM 80 2H HOH 4 0.677 -4.765 5.712 1.00 2.22 H HETATM 81 O HOH 5 3.077 -0.188 1.882 1.00 1.66 O HETATM 82 1H HOH 5 3.377 -1.003 1.437 1.00 2.97 H HETATM 83 2H HOH 5 3.810 0.094 2.414 1.00 2.92 H CONECT 1 2 3 4 23 CONECT 2 1 CONECT 3 1 CONECT 4 1 5 CONECT 5 4 6 45 46 CONECT 6 5 7 8 47 CONECT 7 6 12 CONECT 8 6 9 10 48 CONECT 9 8 49 CONECT 10 8 11 12 50 CONECT 11 10 51 CONECT 12 7 10 13 52 CONECT 13 12 14 22 CONECT 14 13 15 53 CONECT 15 14 16 CONECT 16 15 17 22 CONECT 17 16 18 19 CONECT 18 17 54 55 CONECT 19 17 20 57 CONECT 20 19 21 56 CONECT 21 20 22 CONECT 22 13 16 21 CONECT 23 1 24 CONECT 24 23 25 26 27 CONECT 25 24 CONECT 26 24 CONECT 27 24 28 CONECT 28 27 29 58 59 CONECT 29 28 30 31 60 CONECT 30 29 35 CONECT 31 29 32 33 61 CONECT 32 31 62 CONECT 33 31 34 35 63 CONECT 34 33 64 CONECT 35 30 33 36 65 CONECT 36 35 37 44 CONECT 37 36 38 66 CONECT 38 37 39 42 CONECT 39 38 40 41 CONECT 40 39 CONECT 41 39 67 68 CONECT 42 38 43 69 CONECT 43 42 44 70 CONECT 44 36 43 71 CONECT 45 5 CONECT 46 5 CONECT 47 6 CONECT 48 8 CONECT 49 9 CONECT 50 10 CONECT 51 11 CONECT 52 12 CONECT 53 14 CONECT 54 18 CONECT 55 18 CONECT 56 20 CONECT 57 19 CONECT 58 28 CONECT 59 28 CONECT 60 29 CONECT 61 31 CONECT 62 32 CONECT 63 33 CONECT 64 34 CONECT 65 35 CONECT 66 37 CONECT 67 41 CONECT 68 41 CONECT 69 42 CONECT 70 43 CONECT 71 44 MASTER 183 0 1 0 0 0 0 6 83 0 71 0 END