HEADER LYASE 14-OCT-13 3WJP TITLE CRYSTAL STRUCTURE OF THE HYPE CA FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 GENE: TK1993; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS [NIFE] HYDROGENASE MATURATION, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR T.TOMINAGA,S.WATANABE,K.MIKI REVDAT 4 06-DEC-23 3WJP 1 REMARK REVDAT 3 08-NOV-23 3WJP 1 REMARK LINK REVDAT 2 22-JAN-14 3WJP 1 JRNL REVDAT 1 18-DEC-13 3WJP 0 JRNL AUTH T.TOMINAGA,S.WATANABE,R.MATSUMI,H.ATOMI,T.IMANAKA,K.MIKI JRNL TITL CRYSTAL STRUCTURES OF THE CARBAMOYLATED AND CYANATED FORMS JRNL TITL 2 OF HYPE FOR [NIFE] HYDROGENASE MATURATION JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 20485 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 24297906 JRNL DOI 10.1073/PNAS.1313620110 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 83607 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 4212 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 42.0904 - 4.7598 0.99 2911 132 0.1863 0.1875 REMARK 3 2 4.7598 - 3.7788 1.00 2737 156 0.1418 0.1711 REMARK 3 3 3.7788 - 3.3013 1.00 2743 118 0.1491 0.1480 REMARK 3 4 3.3013 - 2.9996 0.99 2660 175 0.1660 0.1771 REMARK 3 5 2.9996 - 2.7846 1.00 2671 151 0.1670 0.1801 REMARK 3 6 2.7846 - 2.6205 1.00 2695 116 0.1634 0.1912 REMARK 3 7 2.6205 - 2.4892 1.00 2662 136 0.1624 0.1733 REMARK 3 8 2.4892 - 2.3809 1.00 2675 126 0.1676 0.1673 REMARK 3 9 2.3809 - 2.2892 1.00 2651 139 0.1628 0.1582 REMARK 3 10 2.2892 - 2.2103 0.99 2616 151 0.1655 0.1734 REMARK 3 11 2.2103 - 2.1412 1.00 2654 133 0.1703 0.1712 REMARK 3 12 2.1412 - 2.0799 1.00 2624 141 0.1700 0.1931 REMARK 3 13 2.0799 - 2.0252 1.00 2661 139 0.1782 0.1836 REMARK 3 14 2.0252 - 1.9758 1.00 2629 144 0.1756 0.2234 REMARK 3 15 1.9758 - 1.9309 1.00 2629 155 0.1818 0.1703 REMARK 3 16 1.9309 - 1.8898 1.00 2625 134 0.1753 0.2229 REMARK 3 17 1.8898 - 1.8520 1.00 2629 146 0.1748 0.1907 REMARK 3 18 1.8520 - 1.8170 1.00 2622 139 0.1834 0.1878 REMARK 3 19 1.8170 - 1.7846 1.00 2632 131 0.1767 0.2038 REMARK 3 20 1.7846 - 1.7543 1.00 2633 135 0.1875 0.1729 REMARK 3 21 1.7543 - 1.7260 1.00 2622 164 0.1832 0.2232 REMARK 3 22 1.7260 - 1.6995 1.00 2609 138 0.1903 0.2277 REMARK 3 23 1.6995 - 1.6745 1.00 2629 144 0.1905 0.2075 REMARK 3 24 1.6745 - 1.6509 1.00 2595 147 0.1880 0.2088 REMARK 3 25 1.6509 - 1.6286 1.00 2638 130 0.2006 0.2027 REMARK 3 26 1.6286 - 1.6074 1.00 2606 133 0.2037 0.2280 REMARK 3 27 1.6074 - 1.5873 1.00 2640 123 0.2057 0.2021 REMARK 3 28 1.5873 - 1.5682 1.00 2600 161 0.2159 0.2585 REMARK 3 29 1.5682 - 1.5500 1.00 2615 138 0.2165 0.2391 REMARK 3 30 1.5500 - 1.5326 0.95 2482 137 0.2362 0.2710 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 2904 REMARK 3 ANGLE : 1.180 3950 REMARK 3 CHIRALITY : 0.074 439 REMARK 3 PLANARITY : 0.005 519 REMARK 3 DIHEDRAL : 15.234 1126 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 3WJP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000096420. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83617 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 42.075 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 14.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07600 REMARK 200 FOR THE DATA SET : 22.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 14.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.60900 REMARK 200 FOR SHELL : 5.200 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: 3VYT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES-NAOH, 1.4-1.55M AMMONIUM REMARK 280 SULFATE, 1.7%(V/V) POLYETHYLENE GLYCOL 400, 6%(V/V) GLYCEROL, PH REMARK 280 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.00650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.43700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.43700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 78.00975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.43700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.43700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.00325 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.43700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.43700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 78.00975 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.43700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.43700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.00325 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 52.00650 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: 14230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -182.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLY A 2 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 293 CD CE NZ 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 ILE A 140 O HOH A 830 1.97 REMARK 500 NH2 ARG A 122 O2 SO4 A 411 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 4 OD1 ASP A 106 7555 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 LYS A 52 -166.93 -122.74 REMARK 500 LYS A 139 47.72 -81.76 REMARK 500 GLU A 141 -85.86 65.68 REMARK 500 GLU A 141 -62.18 -91.52 REMARK 500 HIS A 154 84.89 -151.57 REMARK 500 PHE A 189 -130.55 -108.42 REMARK 500 THR A 223 -129.98 -82.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 43 OD1 REMARK 620 2 ASP A 84 OD1 94.5 REMARK 620 3 ASP A 221 OD1 90.5 92.9 REMARK 620 4 ANP A 401 O2B 97.1 96.2 167.6 REMARK 620 5 HOH A 501 O 176.9 85.7 86.4 86.0 REMARK 620 6 HOH A 506 O 88.4 174.6 82.5 87.9 91.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 59 OD1 REMARK 620 2 ANP A 401 O2A 171.0 REMARK 620 3 ANP A 401 O1G 99.3 89.0 REMARK 620 4 ANP A 401 O1B 90.2 94.2 82.9 REMARK 620 5 HOH A 503 O 83.7 89.0 165.3 82.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 59 OD2 REMARK 620 2 ASP A 84 OD2 87.7 REMARK 620 3 ANP A 401 O3G 98.8 173.3 REMARK 620 4 ANP A 401 O1B 92.9 88.8 89.1 REMARK 620 5 HOH A 501 O 171.3 87.7 86.2 94.4 REMARK 620 6 HOH A 660 O 89.7 89.0 92.7 176.6 82.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 417 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Z1E RELATED DB: PDB REMARK 900 RELATED ID: 2Z1F RELATED DB: PDB REMARK 900 RELATED ID: 3WJQ RELATED DB: PDB REMARK 900 RELATED ID: 3WJR RELATED DB: PDB DBREF 3WJP A 1 338 UNP Q5JII7 Q5JII7_PYRKO 1 338 SEQRES 1 A 338 MET GLY GLU LYS ILE LYS LEU GLU HIS GLY ALA GLY GLY SEQRES 2 A 338 GLU ILE MET GLU GLU LEU LEU ARG ASP VAL ILE LEU LYS SEQRES 3 A 338 THR LEU THR LEU LYS SER ALA GLY GLY ILE GLY LEU ASP SEQRES 4 A 338 ALA LEU ASP ASP GLY ALA THR ILE PRO PHE GLY ASP LYS SEQRES 5 A 338 HIS ILE VAL PHE THR ILE ASP GLY HIS THR VAL LYS PRO SEQRES 6 A 338 LEU PHE PHE PRO GLY GLY ASP ILE GLY ARG LEU ALA VAL SEQRES 7 A 338 SER GLY THR VAL ASN ASP LEU ALA VAL MET GLY ALA GLU SEQRES 8 A 338 PRO ILE ALA LEU ALA ASN SER MET ILE ILE GLY GLU GLY SEQRES 9 A 338 LEU ASP MET GLU VAL LEU LYS ARG VAL LEU LYS SER MET SEQRES 10 A 338 ASP GLU THR ALA ARG GLU VAL PRO VAL PRO ILE VAL THR SEQRES 11 A 338 GLY ASP THR LYS VAL VAL GLU ASP LYS ILE GLU MET PHE SEQRES 12 A 338 VAL ILE THR ALA GLY ILE GLY ILE ALA GLU HIS PRO VAL SEQRES 13 A 338 SER ASP ALA GLY ALA LYS VAL GLY ASP ALA VAL LEU VAL SEQRES 14 A 338 SER GLY THR ILE GLY ASP HIS GLY ILE ALA LEU MET SER SEQRES 15 A 338 HIS ARG GLU GLY ILE ALA PHE GLU THR GLU LEU LYS SER SEQRES 16 A 338 ASP VAL ALA PRO ILE TRP ASP VAL VAL LYS ALA VAL ALA SEQRES 17 A 338 GLU THR ILE GLY TRP GLU ASN ILE HIS ALA MET LYS ASP SEQRES 18 A 338 PRO THR ARG ALA GLY LEU SER ASN ALA LEU ASN GLU ILE SEQRES 19 A 338 ALA ARG LYS SER ASN VAL GLY ILE LEU VAL ARG GLU ALA SEQRES 20 A 338 ASP ILE PRO ILE ARG PRO GLU VAL ARG ALA ALA SER GLU SEQRES 21 A 338 MET LEU GLY ILE SER PRO TYR ASP VAL ALA ASN GLU GLY SEQRES 22 A 338 LYS VAL VAL MET VAL VAL ALA ARG GLU TYR ALA GLU GLU SEQRES 23 A 338 ALA LEU GLU ALA MET ARG LYS THR GLU LYS GLY ARG ASN SEQRES 24 A 338 ALA ALA ILE ILE GLY GLU VAL ILE ALA ASP TYR ARG GLY SEQRES 25 A 338 LYS VAL LEU LEU GLU THR GLY ILE GLY GLY LYS ARG PHE SEQRES 26 A 338 MET GLU PRO PRO GLU GLY ASP PRO VAL PRO ARG ILE QCS MODRES 3WJP QCS A 338 CYS S-CARBAMOYL-L-CYSTEINE HET QCS A 338 17 HET ANP A 401 31 HET MG A 402 1 HET MG A 403 1 HET MG A 404 1 HET BEN A 405 9 HET BEN A 406 9 HET SO4 A 407 5 HET SO4 A 408 5 HET SO4 A 409 5 HET SO4 A 410 5 HET SO4 A 411 5 HET GOL A 412 6 HET GOL A 413 6 HET GOL A 414 6 HET GOL A 415 6 HET PGE A 416 10 HET PGE A 417 10 HETNAM QCS S-CARBAMOYL-L-CYSTEINE HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM BEN BENZAMIDINE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM PGE TRIETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 QCS C4 H8 N2 O3 S FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 MG 3(MG 2+) FORMUL 6 BEN 2(C7 H8 N2) FORMUL 8 SO4 5(O4 S 2-) FORMUL 13 GOL 4(C3 H8 O3) FORMUL 17 PGE 2(C6 H14 O4) FORMUL 19 HOH *355(H2 O) HELIX 1 1 LYS A 6 ALA A 11 5 6 HELIX 2 2 GLY A 13 VAL A 23 1 11 HELIX 3 3 VAL A 23 LEU A 28 1 6 HELIX 4 4 GLY A 37 LEU A 41 5 5 HELIX 5 5 ILE A 73 VAL A 87 1 15 HELIX 6 6 ASP A 106 VAL A 124 1 19 HELIX 7 7 GLY A 174 GLY A 186 1 13 HELIX 8 8 ILE A 200 GLY A 212 1 13 HELIX 9 9 ALA A 225 ASN A 239 1 15 HELIX 10 10 ALA A 247 ILE A 249 5 3 HELIX 11 11 ARG A 252 GLY A 263 1 12 HELIX 12 12 TYR A 283 LYS A 293 1 11 SHEET 1 A 5 ALA A 45 PHE A 49 0 SHEET 2 A 5 LYS A 52 HIS A 61 -1 O ILE A 54 N ILE A 47 SHEET 3 A 5 MET A 142 ALA A 152 -1 O GLY A 150 N VAL A 55 SHEET 4 A 5 GLU A 91 GLY A 102 -1 N SER A 98 O ILE A 145 SHEET 5 A 5 ILE A 128 VAL A 136 1 O LYS A 134 N ILE A 101 SHEET 1 B 2 PHE A 67 PHE A 68 0 SHEET 2 B 2 GLY A 71 ASP A 72 -1 O GLY A 71 N PHE A 68 SHEET 1 C 7 ILE A 216 LYS A 220 0 SHEET 2 C 7 VAL A 276 VAL A 279 -1 O VAL A 278 N ALA A 218 SHEET 3 C 7 ALA A 166 VAL A 169 -1 N LEU A 168 O MET A 277 SHEET 4 C 7 ALA A 301 ILE A 307 -1 O ILE A 303 N VAL A 167 SHEET 5 C 7 GLY A 241 ARG A 245 -1 N LEU A 243 O GLU A 305 SHEET 6 C 7 VAL A 314 THR A 318 1 O GLU A 317 N VAL A 244 SHEET 7 C 7 GLY A 322 PHE A 325 -1 O ARG A 324 N LEU A 316 LINK C ILE A 337 N AQCS A 338 1555 1555 1.34 LINK C ILE A 337 N BQCS A 338 1555 1555 1.33 LINK OD1 ASP A 43 MG MG A 404 1555 1555 2.05 LINK OD1 ASP A 59 MG MG A 402 1555 1555 1.98 LINK OD2 ASP A 59 MG MG A 403 1555 1555 2.04 LINK OD2 ASP A 84 MG MG A 403 1555 1555 2.08 LINK OD1 ASP A 84 MG MG A 404 1555 1555 2.03 LINK OD1 ASP A 221 MG MG A 404 1555 1555 2.14 LINK O2A ANP A 401 MG MG A 402 1555 1555 2.00 LINK O1G ANP A 401 MG MG A 402 1555 1555 2.05 LINK O1B ANP A 401 MG MG A 402 1555 1555 2.44 LINK O3G ANP A 401 MG MG A 403 1555 1555 2.04 LINK O1B ANP A 401 MG MG A 403 1555 1555 2.26 LINK O2B ANP A 401 MG MG A 404 1555 1555 1.96 LINK MG MG A 402 O HOH A 503 1555 1555 2.05 LINK MG MG A 403 O HOH A 501 1555 1555 2.20 LINK MG MG A 403 O HOH A 660 1555 1555 2.08 LINK MG MG A 404 O HOH A 501 1555 1555 2.17 LINK MG MG A 404 O HOH A 506 1555 1555 2.07 CISPEP 1 LYS A 64 PRO A 65 0 -6.00 CISPEP 2 LYS A 64 PRO A 65 0 -6.64 CISPEP 3 VAL A 124 PRO A 125 0 -6.67 SITE 1 AC1 33 MET A 16 LEU A 20 ILE A 24 LEU A 38 SITE 2 AC1 33 LEU A 41 ASP A 42 ASP A 43 ASP A 59 SITE 3 AC1 33 ASP A 84 ASN A 97 MET A 99 THR A 130 SITE 4 AC1 33 GLY A 131 ASP A 132 THR A 133 LYS A 134 SITE 5 AC1 33 THR A 223 ARG A 224 QCS A 338 MG A 402 SITE 6 AC1 33 MG A 403 MG A 404 HOH A 501 HOH A 503 SITE 7 AC1 33 HOH A 504 HOH A 505 HOH A 506 HOH A 514 SITE 8 AC1 33 HOH A 523 HOH A 525 HOH A 534 HOH A 554 SITE 9 AC1 33 HOH A 660 SITE 1 AC2 5 ASP A 59 ASP A 132 ARG A 224 ANP A 401 SITE 2 AC2 5 HOH A 503 SITE 1 AC3 5 ASP A 59 ASP A 84 ANP A 401 HOH A 501 SITE 2 AC3 5 HOH A 660 SITE 1 AC4 6 ASP A 43 ASP A 84 ASP A 221 ANP A 401 SITE 2 AC4 6 HOH A 501 HOH A 506 SITE 1 AC5 5 LEU A 30 SER A 32 GLU A 190 PRO A 253 SITE 2 AC5 5 GLU A 254 SITE 1 AC6 6 PRO A 48 PHE A 49 ALA A 257 GLU A 260 SITE 2 AC6 6 MET A 261 HOH A 544 SITE 1 AC7 4 ARG A 252 ARG A 298 ASN A 299 HOH A 642 SITE 1 AC8 4 ASP A 309 TYR A 310 ARG A 311 HOH A 680 SITE 1 AC9 1 GLY A 70 SITE 1 BC1 2 ARG A 292 HOH A 669 SITE 1 BC2 3 ARG A 122 HOH A 564 HOH A 749 SITE 1 BC3 11 THR A 172 ASP A 175 LYS A 194 SER A 195 SITE 2 BC3 11 ASP A 196 ARG A 252 LYS A 274 HOH A 507 SITE 3 BC3 11 HOH A 657 HOH A 699 HOH A 802 SITE 1 BC4 4 GLU A 137 PRO A 335 GOL A 415 HOH A 813 SITE 1 BC5 10 SER A 32 ILE A 36 GLY A 37 ASP A 39 SITE 2 BC5 10 ALA A 40 PHE A 189 HOH A 513 HOH A 563 SITE 3 BC5 10 HOH A 720 HOH A 746 SITE 1 BC6 5 LYS A 64 PRO A 65 ARG A 184 GOL A 413 SITE 2 BC6 5 HOH A 528 SITE 1 BC7 6 GLY A 89 ILE A 151 GLU A 153 TRP A 213 SITE 2 BC7 6 HOH A 553 HOH A 826 SITE 1 BC8 7 ARG A 256 SER A 259 GLU A 260 ILE A 264 SITE 2 BC8 7 SER A 265 PRO A 266 TYR A 267 CRYST1 102.874 102.874 104.013 90.00 90.00 90.00 P 43 21 2 8 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 0.009721 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009721 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009614 0.00000