HEADER TRANSFERASE 13-DEC-10 3PYD TITLE CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE TITLE 2 (ISPE) FROM MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ISPE, CMK, 4-(CYTIDINE-5'-DIPHOSPHO)-2-C-METHYL-D-ERYTHRITOL COMPND 5 KINASE; COMPND 6 EC: 2.7.1.148; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: ISPE, RV1011, MT1040, MTCI237.28; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SHAN,X.H.CHEN,T.LIU,H.C.ZHAO,Z.H.RAO,Z.Y.LOU REVDAT 2 01-NOV-23 3PYD 1 REMARK REVDAT 1 25-JAN-12 3PYD 0 JRNL AUTH S.SHAN,X.H.CHEN,T.LIU,H.C.ZHAO,Z.H.RAO,Z.Y.LOU JRNL TITL THE STRUCTURAL BASIS FOR ANTI-TB DRUG DISCOVERY TARGETING OF JRNL TITL 2 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE (ISPE) JRNL TITL 3 FROM MYCOBACTERIUM TUBERCULOSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 23346 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1197 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 37.5756 - 4.3679 0.98 2701 138 0.1857 0.2167 REMARK 3 2 4.3679 - 3.4677 0.99 2595 142 0.1563 0.1911 REMARK 3 3 3.4677 - 3.0296 0.99 2583 123 0.1820 0.2163 REMARK 3 4 3.0296 - 2.7527 0.97 2499 125 0.1968 0.2555 REMARK 3 5 2.7527 - 2.5554 0.96 2461 151 0.2094 0.2808 REMARK 3 6 2.5554 - 2.4048 0.95 2391 149 0.2092 0.2705 REMARK 3 7 2.4048 - 2.2844 0.94 2409 119 0.2107 0.2935 REMARK 3 8 2.2844 - 2.1849 0.91 2300 127 0.2139 0.3083 REMARK 3 9 2.1849 - 2.1008 0.87 2210 123 0.2310 0.2920 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 57.85 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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) : 3.11900 REMARK 3 B22 (A**2) : 0.03990 REMARK 3 B33 (A**2) : -3.15890 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 : 0.008 2188 REMARK 3 ANGLE : 1.177 2987 REMARK 3 CHIRALITY : 0.082 357 REMARK 3 PLANARITY : 0.006 398 REMARK 3 DIHEDRAL : 18.868 779 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3PYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062964. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24569 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1UEK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PROPANE (PH 7.0), 3.2M REMARK 280 NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 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 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 26.29200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.69650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.18750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.69650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.29200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.18750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 PRO A 2 REMARK 465 THR A 3 REMARK 465 GLY A 4 REMARK 465 PRO A 303 REMARK 465 THR A 304 REMARK 465 GLU A 305 REMARK 465 VAL A 306 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 ARG A 24 -149.91 -96.90 REMARK 500 SER A 39 34.20 -79.31 REMARK 500 ASP A 67 -159.64 -132.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1272 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PYE RELATED DB: PDB REMARK 900 RELATED ID: 3PYF RELATED DB: PDB REMARK 900 RELATED ID: 3PYG RELATED DB: PDB DBREF 3PYD A 1 306 UNP P65178 ISPE_MYCTU 1 306 SEQRES 1 A 306 MET PRO THR GLY SER VAL THR VAL ARG VAL PRO GLY LYS SEQRES 2 A 306 VAL ASN LEU TYR LEU ALA VAL GLY ASP ARG ARG GLU ASP SEQRES 3 A 306 GLY TYR HIS GLU LEU THR THR VAL PHE HIS ALA VAL SER SEQRES 4 A 306 LEU VAL ASP GLU VAL THR VAL ARG ASN ALA ASP VAL LEU SEQRES 5 A 306 SER LEU GLU LEU VAL GLY GLU GLY ALA ASP GLN LEU PRO SEQRES 6 A 306 THR ASP GLU ARG ASN LEU ALA TRP GLN ALA ALA GLU LEU SEQRES 7 A 306 MET ALA GLU HIS VAL GLY ARG ALA PRO ASP VAL SER ILE SEQRES 8 A 306 MET ILE ASP LYS SER ILE PRO VAL ALA GLY GLY MET ALA SEQRES 9 A 306 GLY GLY SER ALA ASP ALA ALA ALA VAL LEU VAL ALA MET SEQRES 10 A 306 ASN SER LEU TRP GLU LEU ASN VAL PRO ARG ARG ASP LEU SEQRES 11 A 306 ARG MET LEU ALA ALA ARG LEU GLY SER ASP VAL PRO PHE SEQRES 12 A 306 ALA LEU HIS GLY GLY THR ALA LEU GLY THR GLY ARG GLY SEQRES 13 A 306 GLU GLU LEU ALA THR VAL LEU SER ARG ASN THR PHE HIS SEQRES 14 A 306 TRP VAL LEU ALA PHE ALA ASP SER GLY LEU LEU THR SER SEQRES 15 A 306 ALA VAL TYR ASN GLU LEU ASP ARG LEU ARG GLU VAL GLY SEQRES 16 A 306 ASP PRO PRO ARG LEU GLY GLU PRO GLY PRO VAL LEU ALA SEQRES 17 A 306 ALA LEU ALA ALA GLY ASP PRO ASP GLN LEU ALA PRO LEU SEQRES 18 A 306 LEU GLY ASN GLU MET GLN ALA ALA ALA VAL SER LEU ASP SEQRES 19 A 306 PRO ALA LEU ALA ARG ALA LEU ARG ALA GLY VAL GLU ALA SEQRES 20 A 306 GLY ALA LEU ALA GLY ILE VAL SER GLY SER GLY PRO THR SEQRES 21 A 306 CYS ALA PHE LEU CYS THR SER ALA SER SER ALA ILE ASP SEQRES 22 A 306 VAL GLY ALA GLN LEU SER GLY ALA GLY VAL CYS ARG THR SEQRES 23 A 306 VAL ARG VAL ALA THR GLY PRO VAL PRO GLY ALA ARG VAL SEQRES 24 A 306 VAL SER ALA PRO THR GLU VAL HET GOL A1272 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *190(H2 O) HELIX 1 1 GLY A 60 LEU A 64 5 5 HELIX 2 2 ASN A 70 VAL A 83 1 14 HELIX 3 3 ALA A 104 TRP A 121 1 18 HELIX 4 4 PRO A 126 GLY A 138 1 13 HELIX 5 5 ASP A 140 GLY A 147 1 8 HELIX 6 6 LEU A 180 GLY A 195 1 16 HELIX 7 7 GLU A 202 GLY A 213 1 12 HELIX 8 8 ASP A 214 ALA A 219 1 6 HELIX 9 9 PRO A 220 LEU A 222 5 3 HELIX 10 10 MET A 226 ASP A 234 1 9 HELIX 11 11 PRO A 235 ALA A 247 1 13 HELIX 12 12 SER A 267 GLY A 282 1 16 SHEET 1 A 5 SER A 53 VAL A 57 0 SHEET 2 A 5 VAL A 89 LYS A 95 1 O ILE A 93 N GLU A 55 SHEET 3 A 5 LEU A 31 ASN A 48 -1 N THR A 45 O MET A 92 SHEET 4 A 5 VAL A 6 VAL A 20 -1 N VAL A 6 O VAL A 46 SHEET 5 A 5 GLY A 223 ASN A 224 1 O GLY A 223 N LEU A 16 SHEET 1 B 5 ALA A 160 VAL A 162 0 SHEET 2 B 5 THR A 149 GLY A 152 -1 N THR A 149 O VAL A 162 SHEET 3 B 5 LEU A 31 ASN A 48 -1 N THR A 33 O GLY A 152 SHEET 4 B 5 VAL A 6 VAL A 20 -1 N VAL A 6 O VAL A 46 SHEET 5 B 5 ARG A 298 SER A 301 -1 O VAL A 300 N THR A 7 SHEET 1 C 4 ALA A 251 VAL A 254 0 SHEET 2 C 4 CYS A 261 CYS A 265 -1 O ALA A 262 N ILE A 253 SHEET 3 C 4 PHE A 168 PHE A 174 -1 N VAL A 171 O PHE A 263 SHEET 4 C 4 THR A 286 GLY A 292 -1 O GLY A 292 N PHE A 168 CISPEP 1 GLU A 25 ASP A 26 0 2.98 CISPEP 2 GLY A 258 PRO A 259 0 9.20 CISPEP 3 GLY A 292 PRO A 293 0 -2.11 SITE 1 AC1 10 PRO A 98 ALA A 100 GLY A 101 GLY A 102 SITE 2 AC1 10 MET A 103 ALA A 104 GLY A 105 GLY A 106 SITE 3 AC1 10 HOH A 367 HOH A 433 CRYST1 52.584 72.375 107.393 90.00 90.00 90.00 P 21 21 21 4 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 0.019017 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013817 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009312 0.00000