HEADER TRANSFERASE 15-NOV-11 4A7W TITLE CRYSTAL STRUCTURE OF URIDYLATE KINASE FROM HELICOBACTER PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: URIDYLATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UK, URIDINE MONOPHOSPHATE KINASE, UMP KINASE, UMPK; COMPND 5 EC: 2.7.4.22; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 85962; SOURCE 4 STRAIN: 26695; SOURCE 5 ATCC: 700392D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K-12; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: SG13009; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.H.CHU,P.C.CHEN,M.H.LIU,Y.J.SUN REVDAT 3 20-DEC-23 4A7W 1 REMARK REVDAT 2 11-JUL-12 4A7W 1 JRNL REVDAT 1 27-JUN-12 4A7W 0 JRNL AUTH C.H.CHU,P.C.CHEN,M.H.LIU,Y.C.LI,C.D.HSIAO,Y.J.SUN JRNL TITL STRUCTURES OF HELICOBACTER PYLORI URIDYLATE KINASE: INSIGHT JRNL TITL 2 INTO RELEASE OF THE PRODUCT UDP JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 68 773 2012 JRNL REFN ISSN 0907-4449 JRNL PMID 22751662 JRNL DOI 10.1107/S0907444912011407 REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : LS_WUNIT_K1 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 51379 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2612 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 25.2908 - 3.8711 1.00 5018 276 0.1465 0.1903 REMARK 3 2 3.8711 - 3.0743 1.00 4899 278 0.1607 0.2175 REMARK 3 3 3.0743 - 2.6862 1.00 4886 262 0.1856 0.2515 REMARK 3 4 2.6862 - 2.4408 1.00 4900 252 0.1993 0.2294 REMARK 3 5 2.4408 - 2.2660 1.00 4846 269 0.2052 0.2363 REMARK 3 6 2.2660 - 2.1325 1.00 4895 244 0.2157 0.2444 REMARK 3 7 2.1325 - 2.0257 1.00 4828 268 0.2230 0.2512 REMARK 3 8 2.0257 - 1.9376 1.00 4832 255 0.2263 0.2430 REMARK 3 9 1.9376 - 1.8630 1.00 4847 251 0.2511 0.2405 REMARK 3 10 1.8630 - 1.7988 0.99 4816 257 0.2648 0.2690 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 : 0.36 REMARK 3 B_SOL : 42.26 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.18140 REMARK 3 B22 (A**2) : -1.18140 REMARK 3 B33 (A**2) : 2.36290 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 : 0.006 3539 REMARK 3 ANGLE : 1.038 4781 REMARK 3 CHIRALITY : 0.070 568 REMARK 3 PLANARITY : 0.003 597 REMARK 3 DIHEDRAL : 16.198 1306 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: RESIDUES 1-5 AND 60-68 ARE DISORDERED. REMARK 4 REMARK 4 4A7W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1290050266. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51462 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 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 2BND REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 68.71000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.66974 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 50.96367 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 68.71000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 39.66974 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 50.96367 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 68.71000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 39.66974 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 50.96367 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 68.71000 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 39.66974 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 50.96367 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 68.71000 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 39.66974 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 50.96367 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 68.71000 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 39.66974 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 50.96367 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 79.33947 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 101.92733 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 79.33947 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 101.92733 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 79.33947 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 101.92733 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 79.33947 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 101.92733 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 79.33947 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 101.92733 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 79.33947 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 101.92733 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.6 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 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 B2125 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 MET A 1 REMARK 465 GLN A 2 REMARK 465 ALA A 3 REMARK 465 LYS A 4 REMARK 465 ILE A 5 REMARK 465 ARG A 60 REMARK 465 GLY A 61 REMARK 465 VAL A 62 REMARK 465 SER A 63 REMARK 465 ALA A 64 REMARK 465 ALA A 65 REMARK 465 GLN A 66 REMARK 465 GLY A 67 REMARK 465 GLY A 68 REMARK 465 MET B 1 REMARK 465 GLN B 2 REMARK 465 ALA B 3 REMARK 465 LYS B 4 REMARK 465 ILE B 5 REMARK 465 ARG B 60 REMARK 465 GLY B 61 REMARK 465 VAL B 62 REMARK 465 SER B 63 REMARK 465 ALA B 64 REMARK 465 ALA B 65 REMARK 465 GLN B 66 REMARK 465 GLY B 67 REMARK 465 GLY B 68 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 LYS A 6 CG CD CE NZ REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 LYS A 176 CG CD CE NZ REMARK 470 ASP A 195 CG OD1 OD2 REMARK 470 GLU A 197 CG CD OE1 OE2 REMARK 470 MET A 219 CG SD CE REMARK 470 LYS B 6 CG CD CE NZ REMARK 470 LYS B 165 CG CD CE NZ REMARK 470 LYS B 172 CG CD CE NZ REMARK 470 LYS B 176 CG CD CE NZ REMARK 470 PHE B 177 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP B 195 CG OD1 OD2 REMARK 470 GLU B 197 CG CD OE1 OE2 REMARK 470 MET B 219 CG SD CE 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 PHE A 141 -7.40 70.76 REMARK 500 GLN A 233 -156.93 -128.92 REMARK 500 PHE B 141 -4.38 85.95 REMARK 500 ILE B 193 77.97 -110.06 REMARK 500 GLN B 233 -161.85 -124.80 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 GTP A 1241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1242 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP B 1241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1242 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4A7X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF URIDYLATE KINASE FROM HELICOBACTER PYLORI: REMARK 900 INSIGHT INTO THE REGULATION OF THE PRODUCT UDP RELEASE DBREF 4A7W A 1 240 UNP P56106 PYRH_HELPY 1 240 DBREF 4A7W B 1 240 UNP P56106 PYRH_HELPY 1 240 SEQRES 1 A 240 MET GLN ALA LYS ILE LYS ASN LYS ARG VAL LEU VAL LYS SEQRES 2 A 240 PHE SER GLY GLU ALA LEU ALA GLY ASP ASN GLN PHE GLY SEQRES 3 A 240 ILE ASP ILE HIS VAL LEU ASP HIS ILE ALA LYS GLU ILE SEQRES 4 A 240 LYS SER LEU VAL GLU ASN ASP ILE GLU VAL GLY ILE VAL SEQRES 5 A 240 ILE GLY GLY GLY ASN ILE ILE ARG GLY VAL SER ALA ALA SEQRES 6 A 240 GLN GLY GLY ILE ILE ARG ARG THR SER GLY ASP TYR MET SEQRES 7 A 240 GLY MET LEU ALA THR VAL ILE ASN ALA VAL ALA MET GLN SEQRES 8 A 240 GLU ALA LEU GLU HIS ILE GLY LEU ASP THR ARG VAL GLN SEQRES 9 A 240 SER ALA ILE GLU ILE LYS GLU ILE CYS GLU SER TYR ILE SEQRES 10 A 240 TYR ARG LYS ALA ILE ARG HIS LEU GLU LYS GLY ARG VAL SEQRES 11 A 240 VAL ILE PHE GLY ALA GLY THR GLY ASN PRO PHE PHE THR SEQRES 12 A 240 THR ASP THR ALA ALA THR LEU ARG ALA ILE GLU ILE GLY SEQRES 13 A 240 SER ASP LEU ILE ILE LYS ALA THR LYS VAL ASP GLY ILE SEQRES 14 A 240 TYR ASP LYS ASP PRO ASN LYS PHE LYS ASP ALA LYS LYS SEQRES 15 A 240 LEU ASP THR LEU SER TYR ASN ASP ALA LEU ILE GLY ASP SEQRES 16 A 240 ILE GLU VAL MET ASP ASP THR ALA ILE SER LEU ALA LYS SEQRES 17 A 240 ASP ASN LYS LEU PRO ILE VAL VAL CYS ASN MET PHE LYS SEQRES 18 A 240 LYS GLY ASN LEU LEU GLN VAL ILE LYS HIS GLN GLN GLY SEQRES 19 A 240 VAL PHE SER MET VAL LYS SEQRES 1 B 240 MET GLN ALA LYS ILE LYS ASN LYS ARG VAL LEU VAL LYS SEQRES 2 B 240 PHE SER GLY GLU ALA LEU ALA GLY ASP ASN GLN PHE GLY SEQRES 3 B 240 ILE ASP ILE HIS VAL LEU ASP HIS ILE ALA LYS GLU ILE SEQRES 4 B 240 LYS SER LEU VAL GLU ASN ASP ILE GLU VAL GLY ILE VAL SEQRES 5 B 240 ILE GLY GLY GLY ASN ILE ILE ARG GLY VAL SER ALA ALA SEQRES 6 B 240 GLN GLY GLY ILE ILE ARG ARG THR SER GLY ASP TYR MET SEQRES 7 B 240 GLY MET LEU ALA THR VAL ILE ASN ALA VAL ALA MET GLN SEQRES 8 B 240 GLU ALA LEU GLU HIS ILE GLY LEU ASP THR ARG VAL GLN SEQRES 9 B 240 SER ALA ILE GLU ILE LYS GLU ILE CYS GLU SER TYR ILE SEQRES 10 B 240 TYR ARG LYS ALA ILE ARG HIS LEU GLU LYS GLY ARG VAL SEQRES 11 B 240 VAL ILE PHE GLY ALA GLY THR GLY ASN PRO PHE PHE THR SEQRES 12 B 240 THR ASP THR ALA ALA THR LEU ARG ALA ILE GLU ILE GLY SEQRES 13 B 240 SER ASP LEU ILE ILE LYS ALA THR LYS VAL ASP GLY ILE SEQRES 14 B 240 TYR ASP LYS ASP PRO ASN LYS PHE LYS ASP ALA LYS LYS SEQRES 15 B 240 LEU ASP THR LEU SER TYR ASN ASP ALA LEU ILE GLY ASP SEQRES 16 B 240 ILE GLU VAL MET ASP ASP THR ALA ILE SER LEU ALA LYS SEQRES 17 B 240 ASP ASN LYS LEU PRO ILE VAL VAL CYS ASN MET PHE LYS SEQRES 18 B 240 LYS GLY ASN LEU LEU GLN VAL ILE LYS HIS GLN GLN GLY SEQRES 19 B 240 VAL PHE SER MET VAL LYS HET GTP A1241 32 HET GOL A1242 6 HET GTP B1241 32 HET GOL B1242 6 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GTP 2(C10 H16 N5 O14 P3) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *316(H2 O) HELIX 1 1 SER A 15 GLY A 21 5 7 HELIX 2 2 ASP A 28 ASN A 45 1 18 HELIX 3 3 ARG A 71 ILE A 97 1 27 HELIX 4 4 ILE A 117 LYS A 127 1 11 HELIX 5 5 THR A 143 ILE A 155 1 13 HELIX 6 6 TYR A 188 GLY A 194 1 7 HELIX 7 7 ASP A 200 ASN A 210 1 11 HELIX 8 8 GLY A 223 GLN A 232 1 10 HELIX 9 9 SER B 15 ALA B 20 5 6 HELIX 10 10 ASP B 28 ASN B 45 1 18 HELIX 11 11 ARG B 71 ILE B 97 1 27 HELIX 12 12 ILE B 117 LYS B 127 1 11 HELIX 13 13 THR B 143 ILE B 155 1 13 HELIX 14 14 SER B 187 ILE B 193 1 7 HELIX 15 15 ASP B 200 ASN B 210 1 11 HELIX 16 16 GLY B 223 GLN B 232 1 10 SHEET 1 AA 9 GLU A 114 SER A 115 0 SHEET 2 AA 9 THR A 101 SER A 105 1 O VAL A 103 N GLU A 114 SHEET 3 AA 9 VAL A 130 GLY A 134 1 O VAL A 130 N ARG A 102 SHEET 4 AA 9 GLU A 48 ILE A 53 1 O VAL A 49 N VAL A 131 SHEET 5 AA 9 ARG A 9 PHE A 14 1 O VAL A 10 N GLY A 50 SHEET 6 AA 9 LEU A 159 THR A 164 1 O LEU A 159 N LEU A 11 SHEET 7 AA 9 ILE A 214 ASN A 218 1 O VAL A 215 N LYS A 162 SHEET 8 AA 9 SER A 237 LYS A 240 -1 O SER A 237 N VAL A 216 SHEET 9 AA 9 THR A 185 SER A 187 1 O LEU A 186 N LYS A 240 SHEET 1 AB 2 ILE A 169 TYR A 170 0 SHEET 2 AB 2 LYS A 182 LEU A 183 -1 O LEU A 183 N ILE A 169 SHEET 1 BA 9 GLU B 114 SER B 115 0 SHEET 2 BA 9 THR B 101 SER B 105 1 O VAL B 103 N GLU B 114 SHEET 3 BA 9 VAL B 130 GLY B 134 1 O VAL B 130 N ARG B 102 SHEET 4 BA 9 GLU B 48 ILE B 53 1 O VAL B 49 N VAL B 131 SHEET 5 BA 9 ARG B 9 PHE B 14 1 O VAL B 10 N GLY B 50 SHEET 6 BA 9 LEU B 159 THR B 164 1 O LEU B 159 N LEU B 11 SHEET 7 BA 9 ILE B 214 ASN B 218 1 O VAL B 215 N LYS B 162 SHEET 8 BA 9 SER B 237 VAL B 239 -1 O SER B 237 N VAL B 216 SHEET 9 BA 9 THR B 185 LEU B 186 1 N LEU B 186 O MET B 238 SHEET 1 BB 2 ILE B 169 TYR B 170 0 SHEET 2 BB 2 LYS B 182 LEU B 183 -1 O LEU B 183 N ILE B 169 CISPEP 1 LYS B 176 PHE B 177 0 5.74 SITE 1 AC1 23 ARG A 102 LYS A 110 GLU A 111 ILE A 112 SITE 2 AC1 23 CYS A 113 GLU A 114 ILE A 117 ARG A 119 SITE 3 AC1 23 LYS A 120 ARG A 123 HIS A 124 LYS A 127 SITE 4 AC1 23 ARG A 129 HOH A2064 HOH A2091 HOH A2094 SITE 5 AC1 23 HOH A2096 HOH A2101 HOH A2106 HOH A2162 SITE 6 AC1 23 HOH A2163 HOH A2164 HOH A2165 SITE 1 AC2 10 LYS A 13 SER A 15 GLY A 16 GLU A 17 SITE 2 AC2 10 GLY A 54 GLY A 55 GLY A 56 THR A 144 SITE 3 AC2 10 HOH A2044 HOH A2116 SITE 1 AC3 22 ARG B 102 LYS B 110 GLU B 111 ILE B 112 SITE 2 AC3 22 CYS B 113 GLU B 114 ILE B 117 ARG B 119 SITE 3 AC3 22 LYS B 120 ARG B 123 HIS B 124 LYS B 127 SITE 4 AC3 22 ARG B 129 HOH B2073 HOH B2075 HOH B2083 SITE 5 AC3 22 HOH B2084 HOH B2088 HOH B2148 HOH B2149 SITE 6 AC3 22 HOH B2150 HOH B2151 SITE 1 AC4 9 LYS B 13 SER B 15 GLY B 16 GLU B 17 SITE 2 AC4 9 GLY B 54 GLY B 55 GLY B 56 THR B 144 SITE 3 AC4 9 HOH B2042 CRYST1 137.420 137.420 152.891 90.00 90.00 120.00 H 3 2 36 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 0.007277 0.004201 0.000000 0.00000 SCALE2 0.000000 0.008403 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006541 0.00000