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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
