HEADER LYASE 14-OCT-13 3WJQ TITLE CRYSTAL STRUCTURE OF THE HYPE CN 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 3WJQ 1 REMARK REVDAT 3 08-NOV-23 3WJQ 1 REMARK LINK REVDAT 2 22-JAN-14 3WJQ 1 JRNL REVDAT 1 18-DEC-13 3WJQ 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. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 68178 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 3427 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 42.3977 - 4.7420 0.99 2953 135 0.1879 0.2119 REMARK 3 2 4.7420 - 3.7646 1.00 2782 157 0.1455 0.1861 REMARK 3 3 3.7646 - 3.2890 1.00 2770 126 0.1565 0.1698 REMARK 3 4 3.2890 - 2.9883 1.00 2695 172 0.1717 0.1957 REMARK 3 5 2.9883 - 2.7742 1.00 2713 153 0.1767 0.1806 REMARK 3 6 2.7742 - 2.6106 1.00 2744 115 0.1758 0.2022 REMARK 3 7 2.6106 - 2.4799 1.00 2705 140 0.1721 0.1963 REMARK 3 8 2.4799 - 2.3720 1.00 2710 129 0.1766 0.1769 REMARK 3 9 2.3720 - 2.2807 1.00 2682 144 0.1714 0.1920 REMARK 3 10 2.2807 - 2.2020 1.00 2693 152 0.1733 0.1780 REMARK 3 11 2.2020 - 2.1331 1.00 2677 133 0.1797 0.1885 REMARK 3 12 2.1331 - 2.0722 1.00 2682 143 0.1774 0.2031 REMARK 3 13 2.0722 - 2.0176 1.00 2670 148 0.1802 0.2055 REMARK 3 14 2.0176 - 1.9684 1.00 2687 142 0.1777 0.2228 REMARK 3 15 1.9684 - 1.9236 1.00 2658 149 0.1875 0.1869 REMARK 3 16 1.9236 - 1.8827 1.00 2653 145 0.1880 0.2221 REMARK 3 17 1.8827 - 1.8450 1.00 2672 144 0.1858 0.2125 REMARK 3 18 1.8450 - 1.8102 1.00 2670 147 0.1974 0.2196 REMARK 3 19 1.8102 - 1.7779 1.00 2677 128 0.1965 0.2314 REMARK 3 20 1.7779 - 1.7477 1.00 2666 144 0.2028 0.2171 REMARK 3 21 1.7477 - 1.7196 1.00 2629 160 0.2066 0.2173 REMARK 3 22 1.7196 - 1.6931 1.00 2674 150 0.2159 0.2342 REMARK 3 23 1.6931 - 1.6682 1.00 2662 141 0.2152 0.2465 REMARK 3 24 1.6682 - 1.6447 0.99 2627 130 0.2145 0.2244 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) : 19.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.23 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 : 0.008 2778 REMARK 3 ANGLE : 1.183 3776 REMARK 3 CHIRALITY : 0.077 427 REMARK 3 PLANARITY : 0.005 490 REMARK 3 DIHEDRAL : 14.809 1049 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 3WJQ 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_1000096421. 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 : 68188 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 14.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 27.6500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 14.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.72200 REMARK 200 FOR SHELL : 4.490 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 (%): 67.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.83 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 52.15750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.42300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.42300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 78.23625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.42300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.42300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.07875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.42300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.42300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 78.23625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.42300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.42300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.07875 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 52.15750 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: 14960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -214.0 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 139 CG CD CE NZ REMARK 470 GLU A 153 CG CD OE1 OE2 REMARK 470 ARG A 245 CG CD NE CZ NH1 NH2 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 OD2 ASP A 118 O HOH A 836 2.18 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 2.15 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 -168.56 -122.91 REMARK 500 LYS A 52 -168.56 -123.40 REMARK 500 GLU A 141 -85.18 66.01 REMARK 500 HIS A 154 83.46 -152.02 REMARK 500 PHE A 189 -129.86 -108.57 REMARK 500 THR A 223 -128.91 -79.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 ATP A 411 AND PO4 A 419 ARE IN AN ALTERNATED CONFIGURATION. 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 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 43 OD1 REMARK 620 2 ASP A 84 OD1 99.6 REMARK 620 3 ASP A 221 OD1 88.8 92.6 REMARK 620 4 ATP A 411 O2B 102.1 101.6 160.2 REMARK 620 5 HOH A 659 O 84.9 174.6 84.4 80.3 REMARK 620 6 HOH A 662 O 169.8 88.1 84.2 82.7 87.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 59 OD1 REMARK 620 2 ATP A 411 O1G 99.4 REMARK 620 3 ATP A 411 O1A 168.2 88.4 REMARK 620 4 ATP A 411 O1B 93.4 85.3 96.0 REMARK 620 5 PO4 A 419 O3 82.5 19.5 103.5 96.0 REMARK 620 N 1 2 3 4 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 OD2 REMARK 620 2 ASP A 84 OD2 84.2 REMARK 620 3 ATP A 411 O3G 104.8 171.0 REMARK 620 4 ATP A 411 O1B 93.0 91.9 86.4 REMARK 620 5 PO4 A 419 O1 91.1 166.3 19.6 101.2 REMARK 620 6 HOH A 660 O 87.9 86.9 94.6 178.4 80.1 REMARK 620 7 HOH A 662 O 172.2 92.9 78.4 94.4 90.1 84.7 REMARK 620 N 1 2 3 4 5 6 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 ATP A 411 O2A REMARK 620 2 ATP A 411 O3B 85.3 REMARK 620 3 HOH A 514 O 100.8 159.3 REMARK 620 4 HOH A 629 O 170.7 87.5 84.1 REMARK 620 5 HOH A 832 O 78.4 82.7 79.3 94.8 REMARK 620 6 HOH A 833 O 103.0 114.5 83.6 85.4 162.7 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 MG 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 SO4 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 ATP A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN 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 PEG 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 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 419 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: 3WJP RELATED DB: PDB REMARK 900 RELATED ID: 3WJR RELATED DB: PDB DBREF 3WJQ 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 XCN MODRES 3WJQ XCN A 338 CYS S-CYANO-L-CYSTEINE HET XCN A 338 16 HET MG A 401 1 HET MG A 402 1 HET MG A 403 1 HET MG A 404 1 HET BEN A 405 9 HET SO4 A 406 5 HET SO4 A 407 5 HET SO4 A 408 5 HET SO4 A 409 5 HET SO4 A 410 5 HET ATP A 411 31 HET BEN A 412 9 HET GOL A 413 6 HET GOL A 414 6 HET GOL A 415 6 HET PEG A 416 7 HET PGE A 417 10 HET PGE A 418 10 HET PO4 A 419 5 HETNAM XCN S-CYANO-L-CYSTEINE HETNAM MG MAGNESIUM ION HETNAM BEN BENZAMIDINE HETNAM SO4 SULFATE ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PGE TRIETHYLENE GLYCOL HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 XCN C4 H6 N2 O2 S FORMUL 2 MG 4(MG 2+) FORMUL 6 BEN 2(C7 H8 N2) FORMUL 7 SO4 5(O4 S 2-) FORMUL 12 ATP C10 H16 N5 O13 P3 FORMUL 14 GOL 3(C3 H8 O3) FORMUL 17 PEG C4 H10 O3 FORMUL 18 PGE 2(C6 H14 O4) FORMUL 20 PO4 O4 P 3- FORMUL 21 HOH *339(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 AXCN A 338 1555 1555 1.33 LINK C ILE A 337 N BXCN A 338 1555 1555 1.32 LINK OD1 ASP A 43 MG MG A 403 1555 1555 2.05 LINK OD1 ASP A 59 MG MG A 401 1555 1555 2.00 LINK OD2 ASP A 59 MG MG A 402 1555 1555 2.07 LINK OD2 ASP A 84 MG MG A 402 1555 1555 2.19 LINK OD1 ASP A 84 MG MG A 403 1555 1555 2.06 LINK OD1 ASP A 221 MG MG A 403 1555 1555 2.16 LINK MG MG A 401 O1GAATP A 411 1555 1555 1.98 LINK MG MG A 401 O1AAATP A 411 1555 1555 2.06 LINK MG MG A 401 O1BAATP A 411 1555 1555 2.25 LINK MG MG A 401 O3 BPO4 A 419 1555 1555 2.31 LINK MG MG A 402 O3GAATP A 411 1555 1555 2.06 LINK MG MG A 402 O1BAATP A 411 1555 1555 2.24 LINK MG MG A 402 O1 BPO4 A 419 1555 1555 2.50 LINK MG MG A 402 O HOH A 660 1555 1555 2.15 LINK MG MG A 402 O HOH A 662 1555 1555 2.20 LINK MG MG A 403 O2BAATP A 411 1555 1555 1.93 LINK MG MG A 403 O HOH A 659 1555 1555 2.15 LINK MG MG A 403 O HOH A 662 1555 1555 2.20 LINK MG MG A 404 O2AAATP A 411 1555 1555 2.25 LINK MG MG A 404 O3BAATP A 411 1555 1555 2.45 LINK MG MG A 404 O HOH A 514 1555 1555 2.09 LINK MG MG A 404 O HOH A 629 1555 1555 2.20 LINK MG MG A 404 O HOH A 832 1555 1555 1.83 LINK MG MG A 404 O HOH A 833 1555 1555 2.10 CISPEP 1 LYS A 64 PRO A 65 0 -2.64 CISPEP 2 LYS A 64 PRO A 65 0 -9.16 CISPEP 3 VAL A 124 PRO A 125 0 -6.60 SITE 1 AC1 6 ASP A 59 ASP A 132 ARG A 224 ATP A 411 SITE 2 AC1 6 PO4 A 419 HOH A 661 SITE 1 AC2 6 ASP A 59 ASP A 84 ATP A 411 PO4 A 419 SITE 2 AC2 6 HOH A 660 HOH A 662 SITE 1 AC3 6 ASP A 43 ASP A 84 ASP A 221 ATP A 411 SITE 2 AC3 6 HOH A 659 HOH A 662 SITE 1 AC4 5 ATP A 411 HOH A 514 HOH A 629 HOH A 832 SITE 2 AC4 5 HOH A 833 SITE 1 AC5 7 LEU A 30 SER A 32 PHE A 189 GLU A 190 SITE 2 AC5 7 PRO A 253 GLU A 254 PGE A 417 SITE 1 AC6 4 ARG A 252 ARG A 298 ASN A 299 HOH A 706 SITE 1 AC7 4 ASP A 309 TYR A 310 ARG A 311 HOH A 704 SITE 1 AC8 3 ARG A 292 HOH A 627 HOH A 675 SITE 1 AC9 4 PRO A 69 GLY A 70 LYS A 194 HOH A 652 SITE 1 BC1 2 ARG A 122 HOH A 621 SITE 1 BC2 32 MET A 16 LEU A 20 LEU A 38 LEU A 41 SITE 2 BC2 32 ASP A 42 ASP A 43 ASP A 59 ASP A 84 SITE 3 BC2 32 ASN A 97 MET A 99 THR A 130 GLY A 131 SITE 4 BC2 32 ASP A 132 THR A 133 LYS A 134 THR A 223 SITE 5 BC2 32 ARG A 224 XCN A 338 MG A 401 MG A 402 SITE 6 BC2 32 MG A 403 MG A 404 HOH A 502 HOH A 510 SITE 7 BC2 32 HOH A 525 HOH A 544 HOH A 659 HOH A 660 SITE 8 BC2 32 HOH A 661 HOH A 662 HOH A 784 HOH A 832 SITE 1 BC3 9 PRO A 48 ILE A 93 ILE A 151 ALA A 257 SITE 2 BC3 9 GLU A 260 MET A 261 PGE A 417 HOH A 523 SITE 3 BC3 9 HOH A 815 SITE 1 BC4 10 SER A 32 ILE A 36 GLY A 37 ASP A 39 SITE 2 BC4 10 ALA A 40 PHE A 189 HOH A 519 HOH A 551 SITE 3 BC4 10 HOH A 736 HOH A 819 SITE 1 BC5 3 LYS A 64 PRO A 65 ARG A 184 SITE 1 BC6 11 THR A 172 ASP A 175 LYS A 194 SER A 195 SITE 2 BC6 11 ASP A 196 ARG A 252 LYS A 274 HOH A 506 SITE 3 BC6 11 HOH A 670 HOH A 768 HOH A 811 SITE 1 BC7 2 ARG A 112 HOH A 555 SITE 1 BC8 11 GLU A 91 PRO A 92 PRO A 125 PRO A 253 SITE 2 BC8 11 ARG A 256 ALA A 257 BEN A 405 BEN A 412 SITE 3 BC8 11 HOH A 513 HOH A 669 HOH A 764 SITE 1 BC9 7 ARG A 256 SER A 259 GLU A 260 ILE A 264 SITE 2 BC9 7 SER A 265 PRO A 266 TYR A 267 SITE 1 CC1 10 ASP A 59 ASP A 132 LYS A 134 THR A 223 SITE 2 CC1 10 ARG A 224 XCN A 338 MG A 401 MG A 402 SITE 3 CC1 10 HOH A 660 HOH A 734 CRYST1 102.846 102.846 104.315 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 0.009723 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009723 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009586 0.00000