HEADER HYDROLASE 30-DEC-13 4O8S TITLE CRYSTAL STRUCTURE OF JHP933 FROM HELICOBACTER PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 85963; SOURCE 4 STRAIN: J99 / ATCC 700824; SOURCE 5 GENE: 933, JHP_0933; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-15B KEYWDS NUCLEOTIDYL TRANSFERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.H.ZHAO,Y.T.SU,L.F.SUN,Y.WU REVDAT 1 10-SEP-14 4O8S 0 JRNL AUTH Y.ZHAO,X.YE,Y.SU,L.SUN,F.SHE,Y.WU JRNL TITL CRYSTAL STRUCTURE CONFIRMATION OF JHP933 AS A JRNL TITL 2 NUCLEOTIDYLTRANSFERASE SUPERFAMILY PROTEIN FROM HELICOBACTER JRNL TITL 3 PYLORI STRAIN J99 JRNL REF PLOS ONE V. 9 04609 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 25101777 JRNL DOI 10.1371/JOURNAL.PONE.0104609 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 18941 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.660 REMARK 3 FREE R VALUE TEST SET COUNT : 1829 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 38.0114 - 4.9346 0.99 1366 142 0.1872 0.2091 REMARK 3 2 4.9346 - 3.9180 1.00 1325 148 0.1671 0.1586 REMARK 3 3 3.9180 - 3.4231 1.00 1348 148 0.1940 0.2180 REMARK 3 4 3.4231 - 3.1103 1.00 1310 141 0.2125 0.2467 REMARK 3 5 3.1103 - 2.8874 1.00 1347 143 0.2143 0.2584 REMARK 3 6 2.8874 - 2.7172 1.00 1320 137 0.2299 0.2595 REMARK 3 7 2.7172 - 2.5812 0.99 1315 143 0.2303 0.3252 REMARK 3 8 2.5812 - 2.4689 0.99 1330 139 0.2279 0.2875 REMARK 3 9 2.4689 - 2.3738 0.98 1292 139 0.2261 0.2528 REMARK 3 10 2.3738 - 2.2919 0.99 1306 140 0.2356 0.2868 REMARK 3 11 2.2919 - 2.2203 0.98 1297 140 0.2471 0.2833 REMARK 3 12 2.2203 - 2.1568 0.98 1287 138 0.2493 0.3013 REMARK 3 13 2.1568 - 2.1000 0.95 1269 131 0.2687 0.2933 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 32.44 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.76330 REMARK 3 B22 (A**2) : 1.76330 REMARK 3 B33 (A**2) : -3.52650 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 1893 REMARK 3 ANGLE : 1.137 2543 REMARK 3 CHIRALITY : 0.082 290 REMARK 3 PLANARITY : 0.004 327 REMARK 3 DIHEDRAL : 14.209 732 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 4O8S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JAN-14. REMARK 100 THE RCSB ID CODE IS RCSB084185. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20549 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.13900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.93200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M POTASSIUM SODIUM TARTARATE, 0.1M REMARK 280 TRIS-HCL, 32%(V/W) PEG4000, PH 7.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 47.24467 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 23.62233 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 47.24467 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 23.62233 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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 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 GLU A 124 O HOH A 311 1.90 REMARK 500 OD1 ASP A 57 O HOH A 352 2.01 REMARK 500 O HOH A 375 O HOH A 376 2.10 REMARK 500 NH2 ARG A 117 O HOH A 375 2.15 REMARK 500 OE2 GLU A 113 O HOH A 328 2.16 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 ARG A 117 21.06 49.23 REMARK 500 PHE A 148 -57.28 -136.63 REMARK 500 REMARK 500 REMARK: NULL DBREF 4O8S A 11 242 UNP Q9ZKK2 Q9ZKK2_HELPJ 11 242 SEQRES 1 A 232 SER LEU SER GLU GLN ALA LEU ASN HIS GLU LYS LEU MSE SEQRES 2 A 232 ARG ALA ILE VAL LYS ASN LEU ALA ASP THR PRO MSE VAL SEQRES 3 A 232 LEU LYS GLY GLU THR ALA LEU TYR LEU GLY TYR GLY LEU SEQRES 4 A 232 ASN ARG PHE SER GLU ASP LEU ASP PHE ASP CYS HIS LYS SEQRES 5 A 232 LYS ILE ASN LEU LEU GLY ARG VAL LYS SER ALA ILE PRO SEQRES 6 A 232 ASN GLY ILE ILE LEU ASN ASP ILE HIS ILE LYS LYS ASP SEQRES 7 A 232 THR ASP SER VAL GLY ARG TYR MSE VAL ARG TYR ALA THR SEQRES 8 A 232 LYS ASP ASN LYS GLU GLU GLN THR LEU LYS LEU GLU ILE SEQRES 9 A 232 SER TYR ARG ASP ALA PRO LYS GLU SER GLU VAL ASN VAL SEQRES 10 A 232 ILE GLU GLY MSE ARG ILE ALA LYS ILE GLU ARG ILE ILE SEQRES 11 A 232 ASP ASN LYS LEU CYS ALA CYS PHE ASP GLY GLU HIS THR SEQRES 12 A 232 ARG THR LYS ALA ARG ASP LEU PHE ASP LEU HIS PHE LEU SEQRES 13 A 232 ALA LYS HIS TYR GLU GLU HIS PHE ASN LEU ASP LEU ALA SEQRES 14 A 232 SER ARG LEU LYS ASP PHE SER LYS ASP PRO ASP LYS LEU SEQRES 15 A 232 VAL SER ASP TYR LEU VAL ASP VAL LYS LEU ASP ALA LEU SEQRES 16 A 232 LEU ASN GLN ILE MSE ASP LEU GLU GLU THR ALA LEU GLU SEQRES 17 A 232 LEU GLY VAL MSE ALA GLN LEU ILE HIS LYS LYS LEU GLU SEQRES 18 A 232 LYS GLN SER HIS SER LEU ASN ALA LEU GLN GLU MODRES 4O8S MSE A 23 MET SELENOMETHIONINE MODRES 4O8S MSE A 35 MET SELENOMETHIONINE MODRES 4O8S MSE A 96 MET SELENOMETHIONINE MODRES 4O8S MSE A 131 MET SELENOMETHIONINE MODRES 4O8S MSE A 210 MET SELENOMETHIONINE MODRES 4O8S MSE A 222 MET SELENOMETHIONINE HET MSE A 23 8 HET MSE A 35 8 HET MSE A 96 8 HET MSE A 131 8 HET MSE A 210 8 HET MSE A 222 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 HOH *76(H2 O) HELIX 1 1 SER A 13 LEU A 30 1 18 HELIX 2 2 ALA A 31 THR A 33 5 3 HELIX 3 3 LYS A 38 TYR A 47 1 10 HELIX 4 4 ASN A 65 ILE A 74 1 10 HELIX 5 5 LYS A 121 SER A 123 5 3 HELIX 6 6 LYS A 135 PHE A 148 1 14 HELIX 7 7 LYS A 156 TYR A 170 1 15 HELIX 8 8 GLU A 171 PHE A 174 5 4 HELIX 9 9 ASN A 175 LYS A 187 1 13 HELIX 10 10 ASP A 188 ASP A 203 1 16 HELIX 11 11 ASP A 211 GLU A 242 1 32 SHEET 1 A 5 VAL A 36 LEU A 37 0 SHEET 2 A 5 LEU A 56 CYS A 60 -1 O ASP A 59 N VAL A 36 SHEET 3 A 5 GLN A 108 TYR A 116 1 O LYS A 111 N LEU A 56 SHEET 4 A 5 VAL A 92 THR A 101 -1 N TYR A 99 O GLN A 108 SHEET 5 A 5 ILE A 78 ASP A 88 -1 N ILE A 79 O ALA A 100 SHEET 1 B 2 VAL A 125 ILE A 128 0 SHEET 2 B 2 MSE A 131 ALA A 134 -1 O ILE A 133 N ASN A 126 LINK C LEU A 22 N MSE A 23 1555 1555 1.33 LINK C MSE A 23 N ARG A 24 1555 1555 1.34 LINK C PRO A 34 N MSE A 35 1555 1555 1.33 LINK C MSE A 35 N VAL A 36 1555 1555 1.33 LINK C TYR A 95 N MSE A 96 1555 1555 1.33 LINK C MSE A 96 N VAL A 97 1555 1555 1.33 LINK C GLY A 130 N MSE A 131 1555 1555 1.33 LINK C MSE A 131 N ARG A 132 1555 1555 1.33 LINK C ILE A 209 N MSE A 210 1555 1555 1.32 LINK C MSE A 210 N ASP A 211 1555 1555 1.33 LINK C VAL A 221 N MSE A 222 1555 1555 1.34 LINK C MSE A 222 N ALA A 223 1555 1555 1.33 CISPEP 1 SER A 11 LEU A 12 0 -9.48 CRYST1 90.056 90.056 70.867 90.00 90.00 120.00 P 62 6 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 0.011104 0.006411 0.000000 0.00000 SCALE2 0.000000 0.012822 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014111 0.00000