HEADER LIGASE 09-JUN-11 3SDB TITLE CRYSTAL STRUCTURE OF C176A MUTANT OF GLUTAMINE-DEPENDENT NAD+ TITLE 2 SYNTHETASE FROM M. TUBERCULOSIS IN APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMINE-DEPENDENT NAD(+) SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NAD(+) SYNTHASE [GLUTAMINE-HYDROLYZING]; COMPND 5 EC: 6.3.5.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: MT2513, MTCY428.08, NADE, RV2438C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSMT3 KEYWDS GLUTAMINE-AMIDOTRANSFERASE, GLUTAMINASE, GLUTAMINE-DEPENDENT NAD+ KEYWDS 2 SYNTHETASE, LIGASE, AMMONIA TUNNELING, ATP BINDING, NAD, NUCLEOTIDE KEYWDS 3 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR W.CHUENCHOR,B.GERRATANA REVDAT 3 13-SEP-23 3SDB 1 SEQADV REVDAT 2 08-NOV-17 3SDB 1 REMARK REVDAT 1 11-APR-12 3SDB 0 JRNL AUTH W.CHUENCHOR,T.I.DOUKOV,M.RESTO,A.CHANG,B.GERRATANA JRNL TITL REGULATION OF THE INTERSUBUNIT AMMONIA TUNNEL IN JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS GLUTAMINE-DEPENDENT NAD+ JRNL TITL 3 SYNTHETASE. JRNL REF BIOCHEM.J. V. 443 417 2012 JRNL REFN ISSN 0264-6021 JRNL PMID 22280445 JRNL DOI 10.1042/BJ20112210 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 54342 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2717 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.5486 - 5.3385 0.99 2891 153 0.1916 0.2014 REMARK 3 2 5.3385 - 4.2384 1.00 2774 146 0.1349 0.1475 REMARK 3 3 4.2384 - 3.7029 1.00 2757 144 0.1353 0.1583 REMARK 3 4 3.7029 - 3.3645 1.00 2742 144 0.1523 0.1955 REMARK 3 5 3.3645 - 3.1234 1.00 2749 145 0.1596 0.2153 REMARK 3 6 3.1234 - 2.9393 1.00 2715 143 0.1662 0.1877 REMARK 3 7 2.9393 - 2.7921 1.00 2710 143 0.1637 0.2003 REMARK 3 8 2.7921 - 2.6706 1.00 2696 142 0.1622 0.2080 REMARK 3 9 2.6706 - 2.5678 1.00 2720 142 0.1662 0.2148 REMARK 3 10 2.5678 - 2.4792 1.00 2696 143 0.1568 0.2089 REMARK 3 11 2.4792 - 2.4017 1.00 2711 142 0.1621 0.2351 REMARK 3 12 2.4017 - 2.3330 1.00 2702 143 0.1644 0.2076 REMARK 3 13 2.3330 - 2.2716 1.00 2683 140 0.1698 0.2055 REMARK 3 14 2.2716 - 2.2162 1.00 2707 143 0.1762 0.2199 REMARK 3 15 2.2162 - 2.1658 1.00 2673 141 0.1849 0.2592 REMARK 3 16 2.1658 - 2.1197 1.00 2692 142 0.1867 0.2257 REMARK 3 17 2.1197 - 2.0773 1.00 2694 141 0.1970 0.2212 REMARK 3 18 2.0773 - 2.0381 1.00 2683 142 0.2046 0.2514 REMARK 3 19 2.0381 - 2.0017 0.98 2630 138 0.2255 0.2823 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 45.47 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.78620 REMARK 3 B22 (A**2) : -6.78620 REMARK 3 B33 (A**2) : 13.57230 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.020 5089 REMARK 3 ANGLE : 1.724 6916 REMARK 3 CHIRALITY : 0.140 768 REMARK 3 PLANARITY : 0.009 908 REMARK 3 DIHEDRAL : 13.689 1831 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 0:320) REMARK 3 ORIGIN FOR THE GROUP (A): 16.2698 -27.5061 16.1258 REMARK 3 T TENSOR REMARK 3 T11: 0.2670 T22: 0.2475 REMARK 3 T33: 0.2189 T12: 0.0199 REMARK 3 T13: -0.0033 T23: 0.0227 REMARK 3 L TENSOR REMARK 3 L11: 1.0763 L22: 0.7577 REMARK 3 L33: 0.3577 L12: 0.1611 REMARK 3 L13: 0.0237 L23: -0.1552 REMARK 3 S TENSOR REMARK 3 S11: -0.0040 S12: -0.1164 S13: -0.0504 REMARK 3 S21: 0.1198 S22: -0.0151 S23: -0.0558 REMARK 3 S31: 0.0304 S32: 0.0359 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 321:679) REMARK 3 ORIGIN FOR THE GROUP (A): 58.5396 -16.4683 5.9247 REMARK 3 T TENSOR REMARK 3 T11: 0.1672 T22: 0.3505 REMARK 3 T33: 0.4709 T12: 0.0391 REMARK 3 T13: -0.0233 T23: 0.0526 REMARK 3 L TENSOR REMARK 3 L11: 0.6629 L22: 1.1668 REMARK 3 L33: 0.9562 L12: -0.2286 REMARK 3 L13: -0.0709 L23: -0.0125 REMARK 3 S TENSOR REMARK 3 S11: -0.0160 S12: -0.0391 S13: 0.0162 REMARK 3 S21: -0.0109 S22: -0.0521 S23: -0.4028 REMARK 3 S31: 0.0772 S32: 0.3046 S33: -0.0140 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3SDB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000066064. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54362 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 FOR THE DATA SET : 34.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.40400 REMARK 200 FOR SHELL : 4.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3DLA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE, 5 % GLYCEROL, PH 7.0, EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 89.96850 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 89.96850 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 49.35800 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 89.96850 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 89.96850 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 49.35800 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 89.96850 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 89.96850 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 49.35800 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 89.96850 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 89.96850 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 49.35800 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 89.96850 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 89.96850 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 49.35800 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 89.96850 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 89.96850 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 49.35800 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 89.96850 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 89.96850 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 49.35800 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 89.96850 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 89.96850 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 49.35800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 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 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 70530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 138680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -210.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 991 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1009 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PHE A 402 REMARK 465 ALA A 403 REMARK 465 THR A 404 REMARK 465 GLY A 405 REMARK 465 GLU A 406 REMARK 465 HIS A 407 REMARK 465 THR A 408 REMARK 465 LYS A 409 REMARK 465 GLY A 440 REMARK 465 HIS A 441 REMARK 465 PRO A 442 REMARK 465 TYR A 443 REMARK 465 SER A 444 REMARK 465 VAL A 445 REMARK 465 GLY A 446 REMARK 465 GLU A 447 REMARK 465 LYS A 448 REMARK 465 VAL A 449 REMARK 465 TYR A 450 REMARK 465 ASP A 451 REMARK 465 PRO A 544 REMARK 465 GLU A 545 REMARK 465 LEU A 546 REMARK 465 ILE A 547 REMARK 465 PRO A 548 REMARK 465 THR A 549 REMARK 465 GLY A 550 REMARK 465 GLU A 551 REMARK 465 GLU A 552 REMARK 465 GLU A 553 REMARK 465 LEU A 554 REMARK 465 GLN A 555 REMARK 465 SER A 556 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 334 CD OE1 NE2 REMARK 470 ARG A 417 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 454 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 455 OE1 OE2 REMARK 470 ARG A 473 CZ NH1 NH2 REMARK 470 ARG A 518 NH1 NH2 REMARK 470 GLU A 525 CD OE1 OE2 REMARK 470 GLU A 528 CD OE1 OE2 REMARK 470 GLU A 532 CG CD REMARK 470 LYS A 560 CG CD CE NZ REMARK 470 GLU A 596 CG CD REMARK 470 ARG A 674 NE CZ NH1 NH2 REMARK 470 GLU A 675 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O THR A 492 NE2 GLN A 498 1.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 830 O HOH A 830 15545 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 128 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 269 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 269 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 294 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 294 NE - CZ - NH2 ANGL. DEV. = -8.4 DEGREES REMARK 500 ARG A 354 NE - CZ - NH1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG A 354 NE - CZ - NH2 ANGL. DEV. = -9.9 DEGREES REMARK 500 ARG A 609 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 609 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 61 -125.71 54.37 REMARK 500 ARG A 100 -110.49 52.71 REMARK 500 ARG A 128 -118.03 41.55 REMARK 500 ARG A 143 -157.75 -135.42 REMARK 500 THR A 157 51.99 -110.95 REMARK 500 ASP A 158 37.62 -150.51 REMARK 500 ALA A 176 -107.62 50.46 REMARK 500 SER A 203 72.71 58.27 REMARK 500 HIS A 296 45.71 -107.23 REMARK 500 PHE A 454 -47.81 -27.82 REMARK 500 SER A 491 143.06 164.24 REMARK 500 GLU A 558 -9.52 -51.93 REMARK 500 ALA A 638 72.09 -114.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DLA RELATED DB: PDB REMARK 900 THE WILD TYPE PROTEIN BOUND TO DON AND NAAD+ REMARK 900 RELATED ID: 3SEQ RELATED DB: PDB REMARK 900 THE C176A MUTANT PROTEIN BOUND TO AMPCPP AND NAAD+ REMARK 900 RELATED ID: 3SEZ RELATED DB: PDB REMARK 900 THE C176A MUTANT PROTEIN BOUND TO ATP AND NAAD+ DBREF 3SDB A 1 679 UNP P0A5L6 NADE_MYCTU 1 679 SEQADV 3SDB SER A 0 UNP P0A5L6 EXPRESSION TAG SEQADV 3SDB ALA A 176 UNP P0A5L6 CYS 176 ENGINEERED MUTATION SEQRES 1 A 680 SER MET ASN PHE TYR SER ALA TYR GLN HIS GLY PHE VAL SEQRES 2 A 680 ARG VAL ALA ALA CYS THR HIS HIS THR THR ILE GLY ASP SEQRES 3 A 680 PRO ALA ALA ASN ALA ALA SER VAL LEU ASP MET ALA ARG SEQRES 4 A 680 ALA CYS HIS ASP ASP GLY ALA ALA LEU ALA VAL PHE PRO SEQRES 5 A 680 GLU LEU THR LEU SER GLY TYR SER ILE GLU ASP VAL LEU SEQRES 6 A 680 LEU GLN ASP SER LEU LEU ASP ALA VAL GLU ASP ALA LEU SEQRES 7 A 680 LEU ASP LEU VAL THR GLU SER ALA ASP LEU LEU PRO VAL SEQRES 8 A 680 LEU VAL VAL GLY ALA PRO LEU ARG HIS ARG HIS ARG ILE SEQRES 9 A 680 TYR ASN THR ALA VAL VAL ILE HIS ARG GLY ALA VAL LEU SEQRES 10 A 680 GLY VAL VAL PRO LYS SER TYR LEU PRO THR TYR ARG GLU SEQRES 11 A 680 PHE TYR GLU ARG ARG GLN MET ALA PRO GLY ASP GLY GLU SEQRES 12 A 680 ARG GLY THR ILE ARG ILE GLY GLY ALA ASP VAL ALA PHE SEQRES 13 A 680 GLY THR ASP LEU LEU PHE ALA ALA SER ASP LEU PRO GLY SEQRES 14 A 680 PHE VAL LEU HIS VAL GLU ILE ALA GLU ASP MET PHE VAL SEQRES 15 A 680 PRO MET PRO PRO SER ALA GLU ALA ALA LEU ALA GLY ALA SEQRES 16 A 680 THR VAL LEU ALA ASN LEU SER GLY SER PRO ILE THR ILE SEQRES 17 A 680 GLY ARG ALA GLU ASP ARG ARG LEU LEU ALA ARG SER ALA SEQRES 18 A 680 SER ALA ARG CYS LEU ALA ALA TYR VAL TYR ALA ALA ALA SEQRES 19 A 680 GLY GLU GLY GLU SER THR THR ASP LEU ALA TRP ASP GLY SEQRES 20 A 680 GLN THR MET ILE TRP GLU ASN GLY ALA LEU LEU ALA GLU SEQRES 21 A 680 SER GLU ARG PHE PRO LYS GLY VAL ARG ARG SER VAL ALA SEQRES 22 A 680 ASP VAL ASP THR GLU LEU LEU ARG SER GLU ARG LEU ARG SEQRES 23 A 680 MET GLY THR PHE ASP ASP ASN ARG ARG HIS HIS ARG GLU SEQRES 24 A 680 LEU THR GLU SER PHE ARG ARG ILE ASP PHE ALA LEU ASP SEQRES 25 A 680 PRO PRO ALA GLY ASP ILE GLY LEU LEU ARG GLU VAL GLU SEQRES 26 A 680 ARG PHE PRO PHE VAL PRO ALA ASP PRO GLN ARG LEU GLN SEQRES 27 A 680 GLN ASP CYS TYR GLU ALA TYR ASN ILE GLN VAL SER GLY SEQRES 28 A 680 LEU GLU GLN ARG LEU ARG ALA LEU ASP TYR PRO LYS VAL SEQRES 29 A 680 VAL ILE GLY VAL SER GLY GLY LEU ASP SER THR HIS ALA SEQRES 30 A 680 LEU ILE VAL ALA THR HIS ALA MET ASP ARG GLU GLY ARG SEQRES 31 A 680 PRO ARG SER ASP ILE LEU ALA PHE ALA LEU PRO GLY PHE SEQRES 32 A 680 ALA THR GLY GLU HIS THR LYS ASN ASN ALA ILE LYS LEU SEQRES 33 A 680 ALA ARG ALA LEU GLY VAL THR PHE SER GLU ILE ASP ILE SEQRES 34 A 680 GLY ASP THR ALA ARG LEU MET LEU HIS THR ILE GLY HIS SEQRES 35 A 680 PRO TYR SER VAL GLY GLU LYS VAL TYR ASP VAL THR PHE SEQRES 36 A 680 GLU ASN VAL GLN ALA GLY LEU ARG THR ASP TYR LEU PHE SEQRES 37 A 680 ARG ILE ALA ASN GLN ARG GLY GLY ILE VAL LEU GLY THR SEQRES 38 A 680 GLY ASP LEU SER GLU LEU ALA LEU GLY TRP SER THR TYR SEQRES 39 A 680 GLY VAL GLY ASP GLN MET SER HIS TYR ASN VAL ASN ALA SEQRES 40 A 680 GLY VAL PRO LYS THR LEU ILE GLN HIS LEU ILE ARG TRP SEQRES 41 A 680 VAL ILE SER ALA GLY GLU PHE GLY GLU LYS VAL GLY GLU SEQRES 42 A 680 VAL LEU GLN SER VAL LEU ASP THR GLU ILE THR PRO GLU SEQRES 43 A 680 LEU ILE PRO THR GLY GLU GLU GLU LEU GLN SER SER GLU SEQRES 44 A 680 ALA LYS VAL GLY PRO PHE ALA LEU GLN ASP PHE SER LEU SEQRES 45 A 680 PHE GLN VAL LEU ARG TYR GLY PHE ARG PRO SER LYS ILE SEQRES 46 A 680 ALA PHE LEU ALA TRP HIS ALA TRP ASN ASP ALA GLU ARG SEQRES 47 A 680 GLY ASN TRP PRO PRO GLY PHE PRO LYS SER GLU ARG PRO SEQRES 48 A 680 SER TYR SER LEU ALA GLU ILE ARG HIS TRP LEU GLN ILE SEQRES 49 A 680 PHE VAL GLN ARG PHE TYR SER PHE SER GLN PHE LYS ARG SEQRES 50 A 680 SER ALA LEU PRO ASN GLY PRO LYS VAL SER HIS GLY GLY SEQRES 51 A 680 ALA LEU SER PRO ARG GLY ASP TRP ARG ALA PRO SER ASP SEQRES 52 A 680 MET SER ALA ARG ILE TRP LEU ASP GLN ILE ASP ARG GLU SEQRES 53 A 680 VAL PRO LYS GLY FORMUL 2 HOH *363(H2 O) HELIX 1 1 ALA A 6 HIS A 9 5 4 HELIX 2 2 ASP A 25 ASP A 43 1 19 HELIX 3 3 GLY A 57 LEU A 65 5 9 HELIX 4 4 GLN A 66 ALA A 85 1 20 HELIX 5 5 GLU A 177 VAL A 181 5 5 HELIX 6 6 PRO A 184 GLY A 193 1 10 HELIX 7 7 GLY A 208 CYS A 224 1 17 HELIX 8 8 THR A 276 MET A 286 1 11 HELIX 9 9 MET A 286 HIS A 296 1 11 HELIX 10 10 HIS A 296 SER A 302 1 7 HELIX 11 11 ASP A 332 LEU A 358 1 27 HELIX 12 12 GLY A 370 GLU A 387 1 18 HELIX 13 13 PRO A 390 SER A 392 5 3 HELIX 14 14 ASN A 410 GLY A 420 1 11 HELIX 15 15 ILE A 428 ILE A 439 1 12 HELIX 16 16 VAL A 452 GLY A 474 1 23 HELIX 17 17 ASP A 482 GLY A 489 1 8 HELIX 18 18 PRO A 509 GLY A 524 1 16 HELIX 19 19 GLY A 527 THR A 543 1 17 HELIX 20 20 SER A 557 GLY A 562 1 6 HELIX 21 21 PRO A 563 GLY A 578 1 16 HELIX 22 22 ARG A 580 ASN A 593 1 14 HELIX 23 23 PRO A 605 ARG A 609 5 5 HELIX 24 24 SER A 613 SER A 630 1 18 HELIX 25 25 SER A 632 SER A 637 1 6 HELIX 26 26 ALA A 665 VAL A 676 1 12 SHEET 1 A 3 ALA A 114 PRO A 120 0 SHEET 2 A 3 ARG A 102 HIS A 111 -1 N ALA A 107 O VAL A 119 SHEET 3 A 3 MET A 136 ALA A 137 1 O ALA A 137 N ILE A 103 SHEET 1 B 6 ALA A 114 PRO A 120 0 SHEET 2 B 6 ARG A 102 HIS A 111 -1 N ALA A 107 O VAL A 119 SHEET 3 B 6 VAL A 90 HIS A 99 -1 N VAL A 93 O VAL A 108 SHEET 4 B 6 LEU A 47 VAL A 49 1 N ALA A 48 O VAL A 92 SHEET 5 B 6 PHE A 11 THR A 18 1 N CYS A 17 O VAL A 49 SHEET 6 B 6 ARG A 268 ASP A 275 -1 O VAL A 274 N VAL A 12 SHEET 1 C 2 THR A 126 TYR A 127 0 SHEET 2 C 2 PHE A 130 TYR A 131 -1 O PHE A 130 N TYR A 127 SHEET 1 D 2 THR A 145 ILE A 148 0 SHEET 2 D 2 ALA A 151 ALA A 154 -1 O VAL A 153 N ILE A 146 SHEET 1 E 7 ALA A 255 GLU A 259 0 SHEET 2 E 7 THR A 248 GLU A 252 -1 N ILE A 250 O LEU A 257 SHEET 3 E 7 ALA A 227 ALA A 231 -1 N TYR A 228 O TRP A 251 SHEET 4 E 7 VAL A 196 LEU A 200 1 N LEU A 197 O ALA A 227 SHEET 5 E 7 VAL A 170 ILE A 175 1 N HIS A 172 O ALA A 198 SHEET 6 E 7 LEU A 159 ALA A 163 -1 N PHE A 161 O LEU A 171 SHEET 7 E 7 ARG A 304 PHE A 308 1 O ILE A 306 N LEU A 160 SHEET 1 F 5 THR A 422 GLU A 425 0 SHEET 2 F 5 ILE A 394 ALA A 398 1 N ALA A 396 O THR A 422 SHEET 3 F 5 LYS A 362 GLY A 366 1 N VAL A 363 O LEU A 395 SHEET 4 F 5 GLY A 475 GLY A 479 1 O ILE A 476 N VAL A 364 SHEET 5 F 5 TYR A 502 ASN A 503 1 O TYR A 502 N GLY A 479 CRYST1 179.937 179.937 98.716 90.00 90.00 90.00 I 4 2 2 16 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 0.005558 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005558 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010130 0.00000