HEADER BIOSYNTHETIC PROTEIN 26-FEB-20 6M2A TITLE A NON-HIS-RICH TYPE OF CHIMERIC SIROHYDROCHLORIN NICKELOCHELATASE CFBA TITLE 2 FROM M. JANNASCHII AND M. BARKERI COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIROHYDROCHLORIN COBALTOCHELATASE,SIROHYDROCHLORIN COMPND 3 COBALTOCHELATASE,SIROHYDROCHLORIN COBALTOCHELATASE; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: CBIXS,SIROHYDROCHLORIN NICKELCHELATASE,CBIXS, COMPND 6 SIROHYDROCHLORIN NICKELCHELATASE,CBIXS,SIROHYDROCHLORIN COMPND 7 NICKELCHELATASE; COMPND 8 EC: 4.99.1.3,4.99.1.11; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: THIS CHIMERIC PROTEIN WAS PREPARED BY SUBSTITUTION OF COMPND 11 THE HIS-RICH REGION OF CFBA FROM METHANOCALDOCOCCUS JANNASCHII BY THE COMPND 12 CORRESPONDING NON-HIS-RICH REGION OF CFBA FROM METHANOSARCINA COMPND 13 BARKERI. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII (STRAIN ATCC SOURCE 3 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440), METHANOSARCINA SOURCE 4 BARKERI (STRAIN FUSARO / DSM 804); SOURCE 5 ORGANISM_TAXID: 243232, 269797; SOURCE 6 GENE: CBIX, CFBA, MJ0970, CBIX, CFBA; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: C41 KEYWDS CHELATASE, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.FUJISHIRO REVDAT 3 29-NOV-23 6M2A 1 REMARK REVDAT 2 07-JUL-21 6M2A 1 JRNL REVDAT 1 13-JAN-21 6M2A 0 JRNL AUTH T.FUJISHIRO,S.OGAWA JRNL TITL THE NICKEL-SIROHYDROCHLORIN FORMATION MECHANISM OF THE JRNL TITL 2 ANCESTRAL CLASS II CHELATASE CFBA IN COENZYME F430 JRNL TITL 3 BIOSYNTHESIS. JRNL REF CHEM SCI V. 12 2172 2021 JRNL REFN ISSN 2041-6520 JRNL PMID 34163982 JRNL DOI 10.1039/D0SC05439A REMARK 2 REMARK 2 RESOLUTION. 2.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1-3660 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12484 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 610 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 43.4800 - 3.5400 1.00 2979 154 0.2055 0.2590 REMARK 3 2 3.5400 - 2.8100 1.00 2938 143 0.2130 0.2289 REMARK 3 3 2.8100 - 2.4600 1.00 2999 158 0.1619 0.2067 REMARK 3 4 2.4500 - 2.2300 1.00 2959 155 0.1189 0.1636 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.53 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 1127 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6M2A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300015918. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 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) : 1.000 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR, REMARK 200 LIQUID NITROGEN COOLING REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12499 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 REMARK 200 RESOLUTION RANGE LOW (A) : 43.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.289 REMARK 200 R MERGE (I) : 0.17400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.49 REMARK 200 R MERGE FOR SHELL (I) : 0.87900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.730 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: 2XWS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M AMMONIUM SULFATE, 0.3M NA REMARK 280 -FORMATE, 0.1M TRIS, 3% (W/V) GAMMA-PGA, 10% (W/V) PEG 2000 MME, REMARK 280 PH 7.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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 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 30.30000 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 60.60000 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: 4490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 12 -40.58 71.40 REMARK 500 PHE A 43 -62.88 65.86 REMARK 500 ILE A 48 -55.59 109.12 REMARK 500 ARG A 78 -59.95 -138.00 REMARK 500 ASP A 87 -159.41 -159.91 REMARK 500 ASN A 89 -38.94 63.32 REMARK 500 ASP A 97 51.54 -7.18 REMARK 500 ALA A 111 48.61 -85.35 REMARK 500 PHE B 43 -63.62 58.55 REMARK 500 ARG B 78 -61.30 -139.95 REMARK 500 GLU B 88 -81.76 68.46 REMARK 500 CYS B 91 -41.48 88.55 REMARK 500 ILE B 96 -163.86 -121.25 REMARK 500 ASP B 97 68.90 -25.23 REMARK 500 ALA B 111 49.78 -84.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 201 DBREF 6M2A A 1 86 UNP Q58380 CFBA_METJA 1 86 DBREF 6M2A A 87 101 UNP P61816 CFBA_METBF 90 104 DBREF 6M2A A 102 126 UNP Q58380 CFBA_METJA 119 143 DBREF 6M2A B 1 86 UNP Q58380 CFBA_METJA 1 86 DBREF 6M2A B 87 101 UNP P61816 CFBA_METBF 90 104 DBREF 6M2A B 102 126 UNP Q58380 CFBA_METJA 119 143 SEQRES 1 A 126 MET GLU ALA LEU VAL LEU VAL GLY HIS GLY SER ARG LEU SEQRES 2 A 126 PRO TYR SER LYS GLU LEU LEU VAL LYS LEU ALA GLU LYS SEQRES 3 A 126 VAL LYS GLU ARG ASN LEU PHE PRO ILE VAL GLU ILE GLY SEQRES 4 A 126 LEU MET GLU PHE SER GLU PRO THR ILE PRO GLN ALA VAL SEQRES 5 A 126 LYS LYS ALA ILE GLU GLN GLY ALA LYS ARG ILE ILE VAL SEQRES 6 A 126 VAL PRO VAL PHE LEU ALA HIS GLY ILE HIS THR THR ARG SEQRES 7 A 126 ASP ILE PRO ARG LEU LEU GLY LEU ASP GLU ASN GLY CYS SEQRES 8 A 126 GLY THR LEU GLU ILE ASP GLY LYS THR VAL GLU ILE ILE SEQRES 9 A 126 TYR ARG GLU PRO ILE GLY ALA ASP ASP ARG ILE VAL ASP SEQRES 10 A 126 ILE ILE ILE ASP ARG ALA PHE GLY ARG SEQRES 1 B 126 MET GLU ALA LEU VAL LEU VAL GLY HIS GLY SER ARG LEU SEQRES 2 B 126 PRO TYR SER LYS GLU LEU LEU VAL LYS LEU ALA GLU LYS SEQRES 3 B 126 VAL LYS GLU ARG ASN LEU PHE PRO ILE VAL GLU ILE GLY SEQRES 4 B 126 LEU MET GLU PHE SER GLU PRO THR ILE PRO GLN ALA VAL SEQRES 5 B 126 LYS LYS ALA ILE GLU GLN GLY ALA LYS ARG ILE ILE VAL SEQRES 6 B 126 VAL PRO VAL PHE LEU ALA HIS GLY ILE HIS THR THR ARG SEQRES 7 B 126 ASP ILE PRO ARG LEU LEU GLY LEU ASP GLU ASN GLY CYS SEQRES 8 B 126 GLY THR LEU GLU ILE ASP GLY LYS THR VAL GLU ILE ILE SEQRES 9 B 126 TYR ARG GLU PRO ILE GLY ALA ASP ASP ARG ILE VAL ASP SEQRES 10 B 126 ILE ILE ILE ASP ARG ALA PHE GLY ARG HET SO4 A 201 5 HET SO4 B 201 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *18(H2 O) HELIX 1 AA1 PRO A 14 ASN A 31 1 18 HELIX 2 AA2 ILE A 48 GLN A 58 1 11 HELIX 3 AA3 GLY A 73 ARG A 78 1 6 HELIX 4 AA4 ARG A 78 GLY A 85 1 8 HELIX 5 AA5 ASP A 112 PHE A 124 1 13 HELIX 6 AA6 PRO B 14 ASN B 31 1 18 HELIX 7 AA7 THR B 47 GLN B 58 1 12 HELIX 8 AA8 GLY B 73 ARG B 78 1 6 HELIX 9 AA9 ARG B 78 GLY B 85 1 8 HELIX 10 AB1 ASP B 112 PHE B 124 1 13 SHEET 1 AA1 5 ILE A 35 LEU A 40 0 SHEET 2 AA1 5 GLU A 2 GLY A 8 1 N LEU A 6 O GLU A 37 SHEET 3 AA1 5 ARG A 62 PRO A 67 1 O ILE A 64 N VAL A 5 SHEET 4 AA1 5 LYS A 99 TYR A 105 1 O ILE A 104 N VAL A 65 SHEET 5 AA1 5 LEU A 94 ILE A 96 -1 N ILE A 96 O LYS A 99 SHEET 1 AA2 5 ILE B 35 LEU B 40 0 SHEET 2 AA2 5 GLU B 2 GLY B 8 1 N LEU B 6 O GLU B 37 SHEET 3 AA2 5 ARG B 62 PRO B 67 1 O ILE B 64 N VAL B 5 SHEET 4 AA2 5 LYS B 99 TYR B 105 1 O GLU B 102 N ILE B 63 SHEET 5 AA2 5 LEU B 94 ILE B 96 -1 N LEU B 94 O VAL B 101 CISPEP 1 GLU A 45 PRO A 46 0 2.41 CISPEP 2 GLU B 45 PRO B 46 0 2.14 SITE 1 AC1 8 PHE A 69 ALA A 71 HIS A 72 GLY A 73 SITE 2 AC1 8 ILE A 74 HIS A 75 THR A 76 HOH A 305 SITE 1 AC2 8 PHE B 69 ALA B 71 HIS B 72 GLY B 73 SITE 2 AC2 8 ILE B 74 HIS B 75 THR B 76 HOH B 306 CRYST1 50.210 50.210 90.900 90.00 90.00 120.00 P 31 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.019916 0.011499 0.000000 0.00000 SCALE2 0.000000 0.022997 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011001 0.00000