HEADER LYASE 14-OCT-13 3WJR TITLE CRYSTAL STRUCTURE OF HYPE IN COMPLEX WITH A NUCLEOTIDE 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 3 08-NOV-23 3WJR 1 REMARK REVDAT 2 22-JAN-14 3WJR 1 JRNL REVDAT 1 18-DEC-13 3WJR 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. 1.86 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 47503 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2367 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 47.0134 - 4.7921 1.00 2906 133 0.1914 0.2284 REMARK 3 2 4.7921 - 3.8042 1.00 2724 151 0.1464 0.1804 REMARK 3 3 3.8042 - 3.3235 1.00 2722 125 0.1628 0.1748 REMARK 3 4 3.3235 - 3.0196 1.00 2653 172 0.1756 0.1910 REMARK 3 5 3.0196 - 2.8032 1.00 2679 143 0.1826 0.2110 REMARK 3 6 2.8032 - 2.6380 1.00 2668 119 0.1749 0.2078 REMARK 3 7 2.6380 - 2.5059 1.00 2660 132 0.1657 0.1816 REMARK 3 8 2.5059 - 2.3968 1.00 2667 133 0.1727 0.1816 REMARK 3 9 2.3968 - 2.3045 1.00 2609 140 0.1626 0.1842 REMARK 3 10 2.3045 - 2.2250 1.00 2646 143 0.1696 0.1998 REMARK 3 11 2.2250 - 2.1554 1.00 2650 136 0.1740 0.2290 REMARK 3 12 2.1554 - 2.0938 1.00 2612 134 0.1766 0.2072 REMARK 3 13 2.0938 - 2.0387 1.00 2626 151 0.1816 0.2128 REMARK 3 14 2.0387 - 1.9890 1.00 2609 145 0.1762 0.1984 REMARK 3 15 1.9890 - 1.9438 1.00 2629 135 0.1906 0.2478 REMARK 3 16 1.9438 - 1.9024 1.00 2615 146 0.2089 0.2275 REMARK 3 17 1.9024 - 1.8643 0.94 2461 129 0.2304 0.2451 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.73 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 : 0.007 2655 REMARK 3 ANGLE : 1.123 3602 REMARK 3 CHIRALITY : 0.078 415 REMARK 3 PLANARITY : 0.005 466 REMARK 3 DIHEDRAL : 13.512 983 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 3WJR 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_1000096422. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47503 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07100 REMARK 200 FOR THE DATA SET : 22.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.66000 REMARK 200 FOR SHELL : 4.460 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 (%): 68.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.87 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 7.0, 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 52.86400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.32850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.32850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.29600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.32850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.32850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.43200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.32850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.32850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.29600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.32850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.32850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.43200 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 52.86400 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: 12450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -145.0 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 GLU A 3 CG CD OE1 OE2 REMARK 470 LYS A 6 CE NZ REMARK 470 GLU A 18 CD OE1 OE2 REMARK 470 LYS A 115 CD CE NZ 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 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 O HOH A 774 O HOH A 780 4455 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 -168.55 -121.72 REMARK 500 GLU A 141 -84.50 65.93 REMARK 500 PHE A 189 -131.44 -105.96 REMARK 500 THR A 223 -114.11 -79.75 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 412 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 43 OD1 REMARK 620 2 ASP A 84 OD1 111.0 REMARK 620 3 HOH A 652 O 66.1 142.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 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 PGE A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 412 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: 3WJQ RELATED DB: PDB DBREF 3WJR 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 CYS HET BEN A 401 9 HET BEN A 402 9 HET AMP A 403 23 HET SO4 A 404 5 HET SO4 A 405 5 HET SO4 A 406 5 HET SO4 A 407 5 HET SO4 A 408 5 HET PGE A 409 10 HET GOL A 410 6 HET PEG A 411 7 HET MG A 412 1 HETNAM BEN BENZAMIDINE HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM SO4 SULFATE ION HETNAM PGE TRIETHYLENE GLYCOL HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 BEN 2(C7 H8 N2) FORMUL 4 AMP C10 H14 N5 O7 P FORMUL 5 SO4 5(O4 S 2-) FORMUL 10 PGE C6 H14 O4 FORMUL 11 GOL C3 H8 O3 FORMUL 12 PEG C4 H10 O3 FORMUL 13 MG MG 2+ FORMUL 14 HOH *288(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 SER A 265 VAL A 269 5 5 HELIX 13 13 TYR A 283 THR A 294 1 12 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 OD1 ASP A 43 MG MG A 412 1555 1555 2.39 LINK OD1 ASP A 84 MG MG A 412 1555 1555 2.58 LINK MG MG A 412 O HOH A 652 1555 1555 2.90 CISPEP 1 LYS A 64 PRO A 65 0 -0.57 CISPEP 2 VAL A 124 PRO A 125 0 -6.25 SITE 1 AC1 6 LEU A 30 SER A 32 PHE A 189 GLU A 190 SITE 2 AC1 6 PRO A 253 GLU A 254 SITE 1 AC2 8 ILE A 47 PRO A 48 PHE A 49 ALA A 257 SITE 2 AC2 8 GLU A 260 MET A 261 HOH A 523 HOH A 778 SITE 1 AC3 14 MET A 16 LEU A 20 LEU A 38 LEU A 41 SITE 2 AC3 14 ASP A 42 ASN A 97 THR A 130 GLY A 131 SITE 3 AC3 14 ASP A 132 THR A 133 ARG A 224 HOH A 502 SITE 4 AC3 14 HOH A 510 HOH A 654 SITE 1 AC4 5 PRO A 69 GLY A 70 LYS A 194 HOH A 752 SITE 2 AC4 5 HOH A 776 SITE 1 AC5 4 ARG A 252 ARG A 298 ASN A 299 HOH A 692 SITE 1 AC6 3 ASP A 309 TYR A 310 ARG A 311 SITE 1 AC7 3 ARG A 292 HOH A 623 HOH A 667 SITE 1 AC8 2 ARG A 122 HOH A 714 SITE 1 AC9 4 GLY A 89 ILE A 151 GLU A 153 TRP A 213 SITE 1 BC1 11 GLY A 35 ILE A 36 GLY A 37 ASP A 39 SITE 2 BC1 11 ALA A 40 PHE A 189 HOH A 519 HOH A 549 SITE 3 BC1 11 HOH A 569 HOH A 718 HOH A 781 SITE 1 BC2 6 ARG A 256 SER A 259 GLU A 260 ILE A 264 SITE 2 BC2 6 PRO A 266 HOH A 706 SITE 1 BC3 4 ASP A 43 ASP A 84 ASP A 221 HOH A 652 CRYST1 102.657 102.657 105.728 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 0.009741 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009741 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009458 0.00000