HEADER OXIDOREDUCTASE 06-APR-20 6YKA TITLE ASYMMETRIC [FE]-HYDROGENASE FROM METHANOLACINIA PAYNTERI APO AND IN TITLE 2 COMPLEX WITH FEGP AT 2.1-A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5,10-METHENYLTETRAHYDROMETHANOPTERIN HYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.12.98.2; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE HIS-TAG IS LOCATED IN THE C-TERMINAL SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOLACINIA PAYNTERI G-2000; SOURCE 3 ORGANISM_TAXID: 694436; SOURCE 4 CELL_LINE: /; SOURCE 5 ATCC: /; SOURCE 6 ORGAN: /; SOURCE 7 TISSUE: /; SOURCE 8 CELL: /; SOURCE 9 GENE: HMD; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_ATCC_NUMBER: /; SOURCE 13 EXPRESSION_SYSTEM_ORGAN: /; SOURCE 14 EXPRESSION_SYSTEM_TISSUE: /; SOURCE 15 EXPRESSION_SYSTEM_CELL: /; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 EXPRESSION_SYSTEM_VECTOR: PET-24B(+) KEYWDS [FE]-HYDROGENASE; FEGP COFACTOR; GUANYLYLPYRIDINOL; ASYMMETRY; KEYWDS 2 CONFORMATIONAL CHANGES; GMP, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.WAGNER,G.HUANG,F.J.ARRIAZA-GALLARDO,S.SHIMA REVDAT 2 24-JAN-24 6YKA 1 REMARK REVDAT 1 17-FEB-21 6YKA 0 JRNL AUTH G.HUANG,T.WAGNER,U.DEMMER,E.WARKENTIN,U.ERMLER,S.SHIMA JRNL TITL THE HYDRIDE TRANSFER PROCESS IN NADP-DEPENDENT JRNL TITL 2 METHYLENE-TETRAHYDROMETHANOPTERIN DEHYDROGENASE. JRNL REF J.MOL.BIOL. V. 432 2042 2020 JRNL REFN ESSN 1089-8638 JRNL PMID 32061937 JRNL DOI 10.1016/J.JMB.2020.01.042 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 39126 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 1876 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.15 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2864 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2152 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2739 REMARK 3 BIN R VALUE (WORKING SET) : 0.2136 REMARK 3 BIN FREE R VALUE : 0.2505 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.36 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 125 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5196 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 103 REMARK 3 SOLVENT ATOMS : 224 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.43120 REMARK 3 B22 (A**2) : -0.43120 REMARK 3 B33 (A**2) : 0.86230 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.280 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.241 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.186 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 10851 ; 4.000 ; HARMONIC REMARK 3 BOND ANGLES : 19767 ; 4.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2446 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 1634 ; 20.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 10851 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 750 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 12288 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.01 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 1.66 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.57 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -46.0921 11.8257 -7.6979 REMARK 3 T TENSOR REMARK 3 T11: -0.2230 T22: -0.1117 REMARK 3 T33: -0.0598 T12: 0.0087 REMARK 3 T13: -0.0311 T23: 0.1005 REMARK 3 L TENSOR REMARK 3 L11: 1.6552 L22: 0.6833 REMARK 3 L33: 4.3107 L12: -0.2874 REMARK 3 L13: 0.9763 L23: -0.5334 REMARK 3 S TENSOR REMARK 3 S11: -0.1018 S12: 0.4433 S13: 0.1196 REMARK 3 S21: -0.0084 S22: -0.1082 S23: -0.2302 REMARK 3 S31: 0.2038 S32: 0.7431 S33: 0.2100 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): -58.9737 6.7933 31.6297 REMARK 3 T TENSOR REMARK 3 T11: -0.1897 T22: -0.0320 REMARK 3 T33: -0.1305 T12: 0.1048 REMARK 3 T13: -0.0309 T23: 0.0609 REMARK 3 L TENSOR REMARK 3 L11: 0.8782 L22: 1.9586 REMARK 3 L33: 3.9268 L12: -0.7126 REMARK 3 L13: 0.4865 L23: -1.5091 REMARK 3 S TENSOR REMARK 3 S11: -0.2128 S12: -0.3902 S13: -0.0332 REMARK 3 S21: 0.3758 S22: 0.4246 S23: 0.1660 REMARK 3 S31: -0.1472 S32: -0.6247 S33: -0.2117 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6YKA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292106731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97980 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39181 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 68.833 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05900 REMARK 200 FOR THE DATA SET : 28.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 0.71100 REMARK 200 R SYM FOR SHELL (I) : 0.71100 REMARK 200 FOR SHELL : 1.100 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: 4JJF REMARK 200 REMARK 200 REMARK: TRANSPARENT PRISM SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: [FE]-HYDROGENASE HOLOENZYME FROM M. REMARK 280 PAYNTERI WAS CRYSTALLIZED UNDER 95%N2/5%H2 USING 96-WELL TWO- REMARK 280 DROP MRC CRYSTALLIZATION PLATES (SITTING DROP VAPOR DIFFUSION REMARK 280 METHOD). 0.7 UL OF 25-MG/ML RECONSTITUTED HOLOENZYME WAS MIXED REMARK 280 WITH 0.7-UL RESERVOIR SOLUTION UNDER YELLOW LIGHT AND INCUBATED REMARK 280 UNDER DARK CONDITIONS. THE CRYSTALS GREW WITHIN TWO WEEKS IN 30% REMARK 280 W/V POLYETHYLENE GLYCOL 4000, 200-MM LITHIUM SULFATE AND 100-MM REMARK 280 TRIS PH 8.5 (JBSCREEN WIZARD 3&4 HTS, JENA BIOSCIENCE)., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 283.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-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 59.77900 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 119.55800 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 119.55800 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 59.77900 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: 10930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 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 MET B 1 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 SER A 45 -139.14 51.79 REMARK 500 GLU A 90 -104.14 -127.32 REMARK 500 CYS A 175 -177.52 -171.75 REMARK 500 THR A 176 18.89 45.00 REMARK 500 ALA A 204 177.88 174.03 REMARK 500 SER B 45 -135.81 50.44 REMARK 500 GLU B 90 -104.89 -127.16 REMARK 500 ALA B 174 -151.97 -115.92 REMARK 500 ALA B 204 178.28 174.04 REMARK 500 ASP B 251 -159.58 -82.39 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 FE9 B 403 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 175 SG REMARK 620 2 FE9 B 403 N1 83.8 REMARK 620 3 FE9 B 403 C1F 173.9 90.1 REMARK 620 4 FE9 B 403 C8 83.9 84.8 96.6 REMARK 620 5 FE9 B 403 C2F 95.6 175.3 90.4 90.5 REMARK 620 6 HOH B 504 O 86.9 93.8 92.5 170.8 90.8 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 EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE9 B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 404 DBREF 6YKA A 1 342 PDB 6YKA 6YKA 1 342 DBREF 6YKA B 1 342 PDB 6YKA 6YKA 1 342 SEQRES 1 A 342 MET THR ILE LYS LYS VAL ALA ILE LEU GLY ALA GLY CYS SEQRES 2 A 342 TYR ARG THR HIS SER ALA THR GLY ILE THR ASN PHE ALA SEQRES 3 A 342 ARG ALA CYS GLU VAL ALA GLU MET VAL GLY LYS PRO GLU SEQRES 4 A 342 ILE ALA MET THR HIS SER THR ILE ALA MET ALA ALA GLU SEQRES 5 A 342 LEU LYS TYR LEU ALA GLY ILE ASP ASN ILE VAL ILE SER SEQRES 6 A 342 ASP PRO SER PHE ALA GLY GLU PHE THR VAL VAL LYS ASP SEQRES 7 A 342 PHE ASP TYR ASN GLU VAL ILE LYS ALA HIS LYS GLU ASN SEQRES 8 A 342 PRO GLU THR ILE MET PRO LYS ILE ARG GLU LYS VAL ASN SEQRES 9 A 342 GLU LEU ALA LYS THR VAL PRO LYS PRO PRO LYS GLY ALA SEQRES 10 A 342 ILE HIS PHE VAL HIS PRO GLU ASP LEU GLY LEU LYS VAL SEQRES 11 A 342 THR THR ASP ASP ARG GLU ALA VAL ARG ASP ALA ASP LEU SEQRES 12 A 342 ILE ILE THR TRP LEU PRO LYS GLY ASP MET GLN LYS GLY SEQRES 13 A 342 ILE ILE GLU LYS PHE ALA GLY ASP ILE LYS GLN GLY ALA SEQRES 14 A 342 ILE ILE THR HIS ALA CYS THR ILE PRO THR THR LEU PHE SEQRES 15 A 342 TYR LYS ILE PHE GLU GLU LEU GLY ILE ALA ASP LYS VAL SEQRES 16 A 342 GLU VAL THR SER TYR HIS PRO GLY ALA VAL PRO GLU MET SEQRES 17 A 342 LYS GLY GLN VAL TYR ILE ALA GLU GLY TYR ALA SER GLU SEQRES 18 A 342 GLU ALA ILE ASN THR ILE TYR GLU LEU GLY LYS LYS ALA SEQRES 19 A 342 ARG GLY HIS ALA PHE LYS LEU PRO ALA GLU LEU ILE GLY SEQRES 20 A 342 PRO VAL CYS ASP MET CYS ALA ALA LEU THR ALA ILE THR SEQRES 21 A 342 TYR ALA GLY LEU LEU VAL TYR ARG ASP ALA VAL MET ASN SEQRES 22 A 342 ILE LEU GLY ALA PRO ALA GLY PHE SER GLN MET MET ALA SEQRES 23 A 342 THR GLU SER LEU GLU GLN ILE THR ALA TYR MET LYS LYS SEQRES 24 A 342 VAL GLY ILE LYS ASN LEU GLU GLU ASN LEU ASP PRO GLY SEQRES 25 A 342 VAL PHE LEU GLY THR ALA ASP SER MET ASN PHE GLY PRO SEQRES 26 A 342 ILE ALA GLU ILE LEU PRO THR VAL LEU LYS SER LEU GLU SEQRES 27 A 342 LYS ARG ALA LYS SEQRES 1 B 342 MET THR ILE LYS LYS VAL ALA ILE LEU GLY ALA GLY CYS SEQRES 2 B 342 TYR ARG THR HIS SER ALA THR GLY ILE THR ASN PHE ALA SEQRES 3 B 342 ARG ALA CYS GLU VAL ALA GLU MET VAL GLY LYS PRO GLU SEQRES 4 B 342 ILE ALA MET THR HIS SER THR ILE ALA MET ALA ALA GLU SEQRES 5 B 342 LEU LYS TYR LEU ALA GLY ILE ASP ASN ILE VAL ILE SER SEQRES 6 B 342 ASP PRO SER PHE ALA GLY GLU PHE THR VAL VAL LYS ASP SEQRES 7 B 342 PHE ASP TYR ASN GLU VAL ILE LYS ALA HIS LYS GLU ASN SEQRES 8 B 342 PRO GLU THR ILE MET PRO LYS ILE ARG GLU LYS VAL ASN SEQRES 9 B 342 GLU LEU ALA LYS THR VAL PRO LYS PRO PRO LYS GLY ALA SEQRES 10 B 342 ILE HIS PHE VAL HIS PRO GLU ASP LEU GLY LEU LYS VAL SEQRES 11 B 342 THR THR ASP ASP ARG GLU ALA VAL ARG ASP ALA ASP LEU SEQRES 12 B 342 ILE ILE THR TRP LEU PRO LYS GLY ASP MET GLN LYS GLY SEQRES 13 B 342 ILE ILE GLU LYS PHE ALA GLY ASP ILE LYS GLN GLY ALA SEQRES 14 B 342 ILE ILE THR HIS ALA CYS THR ILE PRO THR THR LEU PHE SEQRES 15 B 342 TYR LYS ILE PHE GLU GLU LEU GLY ILE ALA ASP LYS VAL SEQRES 16 B 342 GLU VAL THR SER TYR HIS PRO GLY ALA VAL PRO GLU MET SEQRES 17 B 342 LYS GLY GLN VAL TYR ILE ALA GLU GLY TYR ALA SER GLU SEQRES 18 B 342 GLU ALA ILE ASN THR ILE TYR GLU LEU GLY LYS LYS ALA SEQRES 19 B 342 ARG GLY HIS ALA PHE LYS LEU PRO ALA GLU LEU ILE GLY SEQRES 20 B 342 PRO VAL CYS ASP MET CYS ALA ALA LEU THR ALA ILE THR SEQRES 21 B 342 TYR ALA GLY LEU LEU VAL TYR ARG ASP ALA VAL MET ASN SEQRES 22 B 342 ILE LEU GLY ALA PRO ALA GLY PHE SER GLN MET MET ALA SEQRES 23 B 342 THR GLU SER LEU GLU GLN ILE THR ALA TYR MET LYS LYS SEQRES 24 B 342 VAL GLY ILE LYS ASN LEU GLU GLU ASN LEU ASP PRO GLY SEQRES 25 B 342 VAL PHE LEU GLY THR ALA ASP SER MET ASN PHE GLY PRO SEQRES 26 B 342 ILE ALA GLU ILE LEU PRO THR VAL LEU LYS SER LEU GLU SEQRES 27 B 342 LYS ARG ALA LYS HET EDO A 401 4 HET EDO A 402 4 HET EDO A 403 4 HET EDO A 404 4 HET PGE A 405 10 HET EDO A 406 4 HET GOL A 407 6 HET GOL A 408 6 HET PGE B 401 10 HET EDO B 402 4 HET FE9 B 403 41 HET GOL B 404 6 HETNAM EDO 1,2-ETHANEDIOL HETNAM PGE TRIETHYLENE GLYCOL HETNAM GOL GLYCEROL HETNAM FE9 IRON-GUANYLYL PYRIDINOL COFACTOR HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 EDO 6(C2 H6 O2) FORMUL 7 PGE 2(C6 H14 O4) FORMUL 9 GOL 3(C3 H8 O3) FORMUL 13 FE9 C21 H23 FE N6 O13 P S 4+ FORMUL 15 HOH *224(H2 O) HELIX 1 AA1 TYR A 14 GLY A 21 1 8 HELIX 2 AA2 PHE A 25 GLY A 36 1 12 HELIX 3 AA3 LYS A 37 ALA A 41 5 5 HELIX 4 AA4 HIS A 44 LEU A 56 1 13 HELIX 5 AA5 PRO A 67 ALA A 70 5 4 HELIX 6 AA6 ASP A 80 LYS A 89 1 10 HELIX 7 AA7 GLU A 90 THR A 94 5 5 HELIX 8 AA8 ILE A 95 VAL A 110 1 16 HELIX 9 AA9 HIS A 122 GLY A 127 5 6 HELIX 10 AB1 ASP A 133 ARG A 139 1 7 HELIX 11 AB2 ASP A 152 ALA A 162 1 11 HELIX 12 AB3 GLY A 163 ILE A 165 5 3 HELIX 13 AB4 PRO A 178 LEU A 189 1 12 HELIX 14 AB5 ILE A 191 ASP A 193 5 3 HELIX 15 AB6 SER A 220 GLY A 236 1 17 HELIX 16 AB7 ALA A 243 ASP A 251 1 9 HELIX 17 AB8 CYS A 253 ILE A 274 1 22 HELIX 18 AB9 PRO A 278 GLY A 301 1 24 HELIX 19 AC1 ASN A 304 LEU A 309 1 6 HELIX 20 AC2 ASP A 310 THR A 317 5 8 HELIX 21 AC3 ALA A 318 ASN A 322 5 5 HELIX 22 AC4 PHE A 323 GLY A 324 5 2 HELIX 23 AC5 PRO A 325 ARG A 340 1 16 HELIX 24 AC6 TYR B 14 GLY B 21 1 8 HELIX 25 AC7 PHE B 25 GLY B 36 1 12 HELIX 26 AC8 LYS B 37 THR B 43 5 7 HELIX 27 AC9 HIS B 44 LEU B 56 1 13 HELIX 28 AD1 PRO B 67 ALA B 70 5 4 HELIX 29 AD2 ASP B 80 LYS B 89 1 10 HELIX 30 AD3 GLU B 90 THR B 94 5 5 HELIX 31 AD4 ILE B 95 VAL B 110 1 16 HELIX 32 AD5 HIS B 122 GLY B 127 5 6 HELIX 33 AD6 ASP B 133 ARG B 139 1 7 HELIX 34 AD7 ASP B 152 ALA B 162 1 11 HELIX 35 AD8 GLY B 163 ILE B 165 5 3 HELIX 36 AD9 PRO B 178 LEU B 189 1 12 HELIX 37 AE1 ILE B 191 ASP B 193 5 3 HELIX 38 AE2 SER B 220 GLY B 236 1 17 HELIX 39 AE3 LEU B 245 ASP B 251 1 7 HELIX 40 AE4 CYS B 253 ILE B 274 1 22 HELIX 41 AE5 PRO B 278 GLY B 301 1 24 HELIX 42 AE6 ASN B 304 LEU B 309 1 6 HELIX 43 AE7 ASP B 310 ASN B 322 5 13 HELIX 44 AE8 PHE B 323 GLU B 328 5 6 HELIX 45 AE9 ILE B 329 ARG B 340 1 12 SHEET 1 AA1 6 LYS A 129 THR A 131 0 SHEET 2 AA1 6 ASN A 61 SER A 65 1 N ILE A 64 O LYS A 129 SHEET 3 AA1 6 LYS A 5 LEU A 9 1 N ILE A 8 O VAL A 63 SHEET 4 AA1 6 LEU A 143 THR A 146 1 O ILE A 145 N LEU A 9 SHEET 5 AA1 6 ALA A 169 HIS A 173 1 O THR A 172 N THR A 146 SHEET 6 AA1 6 VAL A 195 SER A 199 1 O GLU A 196 N ILE A 171 SHEET 1 AA2 2 PHE A 73 VAL A 75 0 SHEET 2 AA2 2 ALA A 117 HIS A 119 1 O HIS A 119 N THR A 74 SHEET 1 AA3 2 VAL A 212 GLU A 216 0 SHEET 2 AA3 2 ALA A 238 PRO A 242 1 O PHE A 239 N ILE A 214 SHEET 1 AA4 6 LYS B 129 THR B 131 0 SHEET 2 AA4 6 ASN B 61 SER B 65 1 N ILE B 64 O LYS B 129 SHEET 3 AA4 6 LYS B 5 LEU B 9 1 N ILE B 8 O VAL B 63 SHEET 4 AA4 6 LEU B 143 THR B 146 1 O ILE B 145 N LEU B 9 SHEET 5 AA4 6 ALA B 169 HIS B 173 1 O THR B 172 N THR B 146 SHEET 6 AA4 6 VAL B 195 SER B 199 1 O GLU B 196 N ILE B 171 SHEET 1 AA5 2 GLU B 72 VAL B 75 0 SHEET 2 AA5 2 GLY B 116 HIS B 119 1 O ALA B 117 N THR B 74 SHEET 1 AA6 2 VAL B 212 GLU B 216 0 SHEET 2 AA6 2 ALA B 238 PRO B 242 1 O PHE B 239 N ILE B 214 LINK SG CYS B 175 FE FE9 B 403 1555 1555 2.64 LINK FE FE9 B 403 O HOH B 504 1555 1555 2.47 CISPEP 1 PRO A 113 PRO A 114 0 1.88 CISPEP 2 PRO B 113 PRO B 114 0 1.62 SITE 1 AC1 2 THR A 16 EDO A 402 SITE 1 AC2 5 THR A 16 HIS A 17 EDO A 401 EDO A 403 SITE 2 AC2 5 HOH A 567 SITE 1 AC3 3 TRP A 147 CYS A 175 EDO A 402 SITE 1 AC4 2 ASP A 319 SER A 320 SITE 1 AC5 5 GLU A 222 THR A 226 LYS A 298 LYS A 299 SITE 2 AC5 5 VAL A 300 SITE 1 AC6 3 GLN A 211 TYR A 213 PHE A 239 SITE 1 AC7 8 GLU A 93 THR A 94 PRO A 97 LYS A 98 SITE 2 AC7 8 ASP A 319 ASN A 322 PRO A 331 HOH A 515 SITE 1 AC8 5 LYS A 37 TYR A 55 ALA A 279 GLY A 280 SITE 2 AC8 5 LYS B 303 SITE 1 AC9 6 LYS A 303 MET B 272 PRO B 278 ALA B 279 SITE 2 AC9 6 GLY B 280 PHE B 281 SITE 1 AD1 3 PHE A 281 LYS B 150 CYS B 175 SITE 1 AD2 23 GLY B 10 GLY B 12 HIS B 17 SER B 65 SITE 2 AD2 23 ASP B 66 PRO B 67 PRO B 113 PRO B 114 SITE 3 AD2 23 ASP B 134 TRP B 147 LEU B 148 PRO B 149 SITE 4 AD2 23 ILE B 157 ALA B 174 CYS B 175 THR B 176 SITE 5 AD2 23 HIS B 201 PRO B 202 GLY B 203 ALA B 204 SITE 6 AD2 23 VAL B 205 HOH B 504 HOH B 535 SITE 1 AD3 3 MET B 272 ASN B 273 GLY B 276 CRYST1 79.481 79.481 179.337 90.00 90.00 120.00 P 31 2 1 12 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 0.012582 0.007264 0.000000 0.00000 SCALE2 0.000000 0.014528 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005576 0.00000