HEADER TRANSFERASE 16-MAR-12 4AND TITLE CRYSTAL FORM II OF THE D93N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE TITLE 2 FROM MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NDK, NDKA, NDP KINASE, NUCLEOSIDE-2-P KINASE; COMPND 5 EC: 2.7.4.6; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET24 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.GEORGESCAULD,L.MOYNIE,J.HABERSETZER,I.LASCU,A.DAUTANT REVDAT 3 20-DEC-23 4AND 1 REMARK REVDAT 2 03-APR-13 4AND 1 JRNL REVDAT 1 13-MAR-13 4AND 0 JRNL AUTH F.GEORGESCAULD,L.MOYNIE,J.HABERSETZER,L.CERVONI,I.MOCAN, JRNL AUTH 2 T.BORZA,P.HARRIS,A.DAUTANT,I.LASCU JRNL TITL INTERSUBUNIT IONIC INTERACTIONS STABILIZE THE NUCLEOSIDE JRNL TITL 2 DIPHOSPHATE KINASE OF MYCOBACTERIUM TUBERCULOSIS. JRNL REF PLOS ONE V. 8 57867 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 23526954 JRNL DOI 10.1371/JOURNAL.PONE.0057867 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.CHEN,S.MORERA,J.MOCAN,I.LASCU,J.JANIN REMARK 1 TITL X-RAY STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS NUCLEOSIDE REMARK 1 TITL 2 DIPHOSPHATE KINASE. REMARK 1 REF PROTEINS V. 47 556 2002 REMARK 1 REFN ISSN 0887-3585 REMARK 1 PMID 12001234 REMARK 1 DOI 10.1002/PROT.10113 REMARK 2 REMARK 2 RESOLUTION. 2.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.110 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 10557 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 502 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 26.2966 - 4.4517 1.00 2621 120 0.1935 0.2147 REMARK 3 2 4.4517 - 3.5362 1.00 2494 148 0.2056 0.2336 REMARK 3 3 3.5362 - 3.0900 1.00 2503 123 0.2490 0.3102 REMARK 3 4 3.0900 - 2.8078 0.97 2437 111 0.3451 0.4116 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.40 REMARK 3 SHRINKAGE RADIUS : 1.17 REMARK 3 K_SOL : 0.31 REMARK 3 B_SOL : 50.72 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 69.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.83 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 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 : 0.003 1985 REMARK 3 ANGLE : 0.765 2696 REMARK 3 CHIRALITY : 0.046 324 REMARK 3 PLANARITY : 0.003 354 REMARK 3 DIHEDRAL : 14.104 710 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESI 2:43) REMARK 3 ORIGIN FOR THE GROUP (A): 26.5813 2.8836 -10.6243 REMARK 3 T TENSOR REMARK 3 T11: 0.2450 T22: 0.2982 REMARK 3 T33: 0.3458 T12: -0.0764 REMARK 3 T13: 0.1221 T23: -0.1064 REMARK 3 L TENSOR REMARK 3 L11: 1.7400 L22: 4.1027 REMARK 3 L33: 0.6633 L12: 1.7905 REMARK 3 L13: 0.4618 L23: -0.7679 REMARK 3 S TENSOR REMARK 3 S11: -0.1209 S12: -0.3495 S13: 0.0222 REMARK 3 S21: -0.2926 S22: 0.1381 S23: -0.1896 REMARK 3 S31: 0.1111 S32: -0.1158 S33: 0.0034 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESI 44:64) REMARK 3 ORIGIN FOR THE GROUP (A): 13.7257 -2.4435 -24.4270 REMARK 3 T TENSOR REMARK 3 T11: 0.3401 T22: 0.6180 REMARK 3 T33: 0.4635 T12: -0.1437 REMARK 3 T13: -0.1236 T23: -0.2144 REMARK 3 L TENSOR REMARK 3 L11: 2.3084 L22: 8.3844 REMARK 3 L33: 1.9972 L12: 1.8714 REMARK 3 L13: -1.4012 L23: 1.5249 REMARK 3 S TENSOR REMARK 3 S11: 0.5218 S12: -0.6219 S13: -0.1842 REMARK 3 S21: -0.7127 S22: -1.2628 S23: 0.8258 REMARK 3 S31: -0.2328 S32: 0.8234 S33: 0.3902 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESI 65:136) REMARK 3 ORIGIN FOR THE GROUP (A): 22.6855 6.7325 -16.7100 REMARK 3 T TENSOR REMARK 3 T11: 0.2257 T22: 0.4371 REMARK 3 T33: 0.3459 T12: -0.1132 REMARK 3 T13: 0.0564 T23: -0.1039 REMARK 3 L TENSOR REMARK 3 L11: 0.7991 L22: 2.4235 REMARK 3 L33: 2.3619 L12: 1.7102 REMARK 3 L13: -0.6047 L23: -0.2843 REMARK 3 S TENSOR REMARK 3 S11: -0.0120 S12: 0.2238 S13: 0.2797 REMARK 3 S21: -0.1788 S22: 0.0121 S23: 0.5008 REMARK 3 S31: 0.1458 S32: -0.6928 S33: 0.0388 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESI 2:43) REMARK 3 ORIGIN FOR THE GROUP (A): 33.8303 -3.3860 -1.1889 REMARK 3 T TENSOR REMARK 3 T11: 0.3972 T22: 0.2663 REMARK 3 T33: 0.3499 T12: -0.0895 REMARK 3 T13: 0.1402 T23: -0.0511 REMARK 3 L TENSOR REMARK 3 L11: 2.9449 L22: 0.0620 REMARK 3 L33: 2.8436 L12: 0.1615 REMARK 3 L13: -1.7419 L23: -0.4530 REMARK 3 S TENSOR REMARK 3 S11: -0.0714 S12: -0.1327 S13: -0.0745 REMARK 3 S21: -0.2140 S22: 0.1702 S23: -0.0393 REMARK 3 S31: 0.4349 S32: 0.0711 S33: 0.0223 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESI 44:64) REMARK 3 ORIGIN FOR THE GROUP (A): 29.7291 -8.0720 16.4140 REMARK 3 T TENSOR REMARK 3 T11: 1.4254 T22: 0.7598 REMARK 3 T33: 0.7787 T12: 0.0666 REMARK 3 T13: 0.5663 T23: 0.2958 REMARK 3 L TENSOR REMARK 3 L11: 0.4166 L22: 2.0148 REMARK 3 L33: 3.6647 L12: -0.1437 REMARK 3 L13: 0.9870 L23: -0.6887 REMARK 3 S TENSOR REMARK 3 S11: 0.4305 S12: 0.2033 S13: -0.1076 REMARK 3 S21: -0.1328 S22: -0.3484 S23: 0.5209 REMARK 3 S31: 1.2011 S32: 0.4461 S33: 0.2568 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESI 65:136) REMARK 3 ORIGIN FOR THE GROUP (A): 38.4209 -6.6885 4.7131 REMARK 3 T TENSOR REMARK 3 T11: 0.5365 T22: 0.2985 REMARK 3 T33: 0.3299 T12: -0.0972 REMARK 3 T13: 0.1342 T23: 0.0567 REMARK 3 L TENSOR REMARK 3 L11: 3.0236 L22: 2.4366 REMARK 3 L33: 1.6005 L12: 1.5404 REMARK 3 L13: -1.2586 L23: -2.0995 REMARK 3 S TENSOR REMARK 3 S11: -0.1039 S12: -0.3536 S13: -0.4122 REMARK 3 S21: 0.7285 S22: -0.0166 S23: -0.1556 REMARK 3 S31: 0.3934 S32: 0.1458 S33: 0.1990 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESI 2:43 OR RESI 65:136) REMARK 3 AND (NAME C OR NAME O OR NAME CA OR NAME REMARK 3 CB OR NAME N )) REMARK 3 SELECTION : (CHAIN B AND (RESI 2:43 OR RESI 65:136) REMARK 3 AND (NAME C OR NAME O OR NAME CA OR NAME REMARK 3 CB OR NAME N )) REMARK 3 ATOM PAIRS NUMBER : 559 REMARK 3 RMSD : 0.020 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4AND COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1290051465. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10722 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.810 REMARK 200 RESOLUTION RANGE LOW (A) : 26.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1K44 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, 2% (V/V) REMARK 280 PEG400, 0.1 M HEPES, PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+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 54.20950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.20950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.20950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.20950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 54.20950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.20950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 54.20950 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 54.20950 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 54.20950 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 54.20950 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 54.20950 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 54.20950 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 54.20950 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 54.20950 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 54.20950 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 54.20950 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 54.20950 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 54.20950 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 0.000000 -1.000000 0.000000 54.20950 REMARK 350 BIOMT2 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 2 1.000000 0.000000 0.000000 -54.20950 REMARK 350 BIOMT1 3 0.000000 0.000000 1.000000 54.20950 REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 54.20950 REMARK 350 BIOMT3 3 0.000000 -1.000000 0.000000 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 B2006 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 93 TO ASN REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ASP 93 TO ASN 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 MET A 1 REMARK 465 MET B 1 REMARK 465 HIS B 53 REMARK 465 GLU B 54 REMARK 465 GLY B 55 REMARK 465 LYS B 56 REMARK 465 PRO B 57 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 GLU A 52 CG CD OE1 OE2 REMARK 470 HIS A 53 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 54 CG CD OE1 OE2 REMARK 470 LYS A 56 CG CD CE NZ REMARK 470 PRO A 57 CG CD REMARK 470 PHE A 58 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 52 CG CD OE1 OE2 REMARK 470 PHE B 58 CG CD1 CD2 CE1 CE2 CZ 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 LYS A 56 158.73 -43.76 REMARK 500 ALA A 97 -58.78 -122.48 REMARK 500 PHE A 113 64.90 -100.49 REMARK 500 LEU A 115 -40.66 73.38 REMARK 500 ALA B 97 -58.34 -122.73 REMARK 500 PHE B 113 65.55 -101.25 REMARK 500 LEU B 115 -41.30 73.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K44 RELATED DB: PDB REMARK 900 MYCOBACTERIUM TUBERCULOSIS NUCLEOSIDE DIPHOSPHATE KINASE REMARK 900 RELATED ID: 4ANC RELATED DB: PDB REMARK 900 CRYSTAL FORM I OF THE D93N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE REMARK 900 FROM MYCOBACTERIUM TUBERCULOSIS REMARK 900 RELATED ID: 4ANE RELATED DB: PDB REMARK 900 R80N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYCOBACTERIUM REMARK 900 TUBERCULOSIS DBREF 4AND A 1 136 UNP P84284 NDK_MYCTU 1 136 DBREF 4AND B 1 136 UNP P84284 NDK_MYCTU 1 136 SEQADV 4AND ASN A 93 UNP P84284 ASP 93 ENGINEERED MUTATION SEQADV 4AND ASN B 93 UNP P84284 ASP 93 ENGINEERED MUTATION SEQRES 1 A 136 MET THR GLU ARG THR LEU VAL LEU ILE LYS PRO ASP GLY SEQRES 2 A 136 ILE GLU ARG GLN LEU ILE GLY GLU ILE ILE SER ARG ILE SEQRES 3 A 136 GLU ARG LYS GLY LEU THR ILE ALA ALA LEU GLN LEU ARG SEQRES 4 A 136 THR VAL SER ALA GLU LEU ALA SER GLN HIS TYR ALA GLU SEQRES 5 A 136 HIS GLU GLY LYS PRO PHE PHE GLY SER LEU LEU GLU PHE SEQRES 6 A 136 ILE THR SER GLY PRO VAL VAL ALA ALA ILE VAL GLU GLY SEQRES 7 A 136 THR ARG ALA ILE ALA ALA VAL ARG GLN LEU ALA GLY GLY SEQRES 8 A 136 THR ASN PRO VAL GLN ALA ALA ALA PRO GLY THR ILE ARG SEQRES 9 A 136 GLY ASP PHE ALA LEU GLU THR GLN PHE ASN LEU VAL HIS SEQRES 10 A 136 GLY SER ASP SER ALA GLU SER ALA GLN ARG GLU ILE ALA SEQRES 11 A 136 LEU TRP PHE PRO GLY ALA SEQRES 1 B 136 MET THR GLU ARG THR LEU VAL LEU ILE LYS PRO ASP GLY SEQRES 2 B 136 ILE GLU ARG GLN LEU ILE GLY GLU ILE ILE SER ARG ILE SEQRES 3 B 136 GLU ARG LYS GLY LEU THR ILE ALA ALA LEU GLN LEU ARG SEQRES 4 B 136 THR VAL SER ALA GLU LEU ALA SER GLN HIS TYR ALA GLU SEQRES 5 B 136 HIS GLU GLY LYS PRO PHE PHE GLY SER LEU LEU GLU PHE SEQRES 6 B 136 ILE THR SER GLY PRO VAL VAL ALA ALA ILE VAL GLU GLY SEQRES 7 B 136 THR ARG ALA ILE ALA ALA VAL ARG GLN LEU ALA GLY GLY SEQRES 8 B 136 THR ASN PRO VAL GLN ALA ALA ALA PRO GLY THR ILE ARG SEQRES 9 B 136 GLY ASP PHE ALA LEU GLU THR GLN PHE ASN LEU VAL HIS SEQRES 10 B 136 GLY SER ASP SER ALA GLU SER ALA GLN ARG GLU ILE ALA SEQRES 11 B 136 LEU TRP PHE PRO GLY ALA FORMUL 3 HOH *26(H2 O) HELIX 1 1 LYS A 10 ARG A 16 1 7 HELIX 2 2 LEU A 18 GLY A 30 1 13 HELIX 3 3 SER A 42 TYR A 50 1 9 HELIX 4 4 ALA A 51 GLU A 54 5 4 HELIX 5 5 PHE A 58 THR A 67 1 10 HELIX 6 6 ARG A 80 GLY A 90 1 11 HELIX 7 7 THR A 102 ALA A 108 1 7 HELIX 8 8 SER A 121 PHE A 133 1 13 HELIX 9 9 LYS B 10 ARG B 16 1 7 HELIX 10 10 LEU B 18 GLY B 30 1 13 HELIX 11 11 SER B 42 TYR B 50 1 9 HELIX 12 12 PHE B 58 THR B 67 1 10 HELIX 13 13 ARG B 80 GLY B 90 1 11 HELIX 14 14 THR B 102 ALA B 108 1 7 HELIX 15 15 SER B 121 PHE B 133 1 13 SHEET 1 AA 4 THR A 32 ARG A 39 0 SHEET 2 AA 4 VAL A 71 GLY A 78 -1 O VAL A 71 N ARG A 39 SHEET 3 AA 4 GLU A 3 ILE A 9 -1 O GLU A 3 N GLY A 78 SHEET 4 AA 4 VAL A 116 GLY A 118 -1 O HIS A 117 N LEU A 8 SHEET 1 BA 4 THR B 32 ARG B 39 0 SHEET 2 BA 4 VAL B 71 GLY B 78 -1 O VAL B 71 N ARG B 39 SHEET 3 BA 4 GLU B 3 ILE B 9 -1 O GLU B 3 N GLY B 78 SHEET 4 BA 4 VAL B 116 GLY B 118 -1 O HIS B 117 N LEU B 8 CRYST1 108.419 108.419 108.419 90.00 90.00 90.00 P 21 3 24 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 0.009223 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009223 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009223 0.00000