HEADER ELECTRON TRANSPORT 27-NOV-24 9KRC TITLE CRYSTAL STRUCTURE OF OXIDIIZED CYTOCHROME C6 FROM SYNECHOCOCCUS TITLE 2 ELONGATUS PCC 7942 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C6; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CYTOCHROME C-553,CYTOCHROME C553,SOLUBLE CYTOCHROME F; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS ELONGATUS PCC 7942 = FACHB-805; SOURCE 3 ORGANISM_COMMON: ANACYSTIS NIDULANS R2; SOURCE 4 ORGANISM_TAXID: 1140; SOURCE 5 GENE: PETJ, CYTA, SYNPCC7942_1630; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ELECTRON TRANSPORT PROTEIN, CYTOCHROME-C6, OXIDIIZED STATE, ELECTRON KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR B.T.ZHANG,S.W.LIU,Y.C.XU,W.SHENG,Y.GONG,P.CAO REVDAT 2 05-FEB-25 9KRC 1 JRNL REVDAT 1 29-JAN-25 9KRC 0 JRNL AUTH B.ZHANG,Y.XU,S.LIU,S.CHEN,W.ZHAO,Z.LI,J.WANG,W.ZHAO,H.ZHANG, JRNL AUTH 2 Y.DONG,Y.GONG,W.SHENG,P.CAO JRNL TITL A HIGH-RESOLUTION CRYSTALLOGRAPHIC STUDY OF CYTOCHROME C6: JRNL TITL 2 STRUCTURAL BASIS FOR ELECTRON TRANSFER IN CYANOBACTERIAL JRNL TITL 3 PHOTOSYNTHESIS. JRNL REF INT J MOL SCI V. 26 2025 JRNL REFN ESSN 1422-0067 JRNL PMID 39859539 JRNL DOI 10.3390/IJMS26020824 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 35713 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.220 REMARK 3 FREE R VALUE TEST SET COUNT : 1508 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 41.5200 - 3.1100 1.00 3318 143 0.1542 0.1912 REMARK 3 2 3.1100 - 2.4700 1.00 3159 140 0.1630 0.1598 REMARK 3 3 2.4700 - 2.1600 1.00 3127 140 0.1424 0.1628 REMARK 3 4 2.1600 - 1.9600 1.00 3126 134 0.1354 0.1633 REMARK 3 5 1.9600 - 1.8200 1.00 3101 142 0.1419 0.1623 REMARK 3 6 1.8200 - 1.7100 1.00 3086 137 0.1346 0.1647 REMARK 3 7 1.7100 - 1.6300 1.00 3075 134 0.1224 0.1474 REMARK 3 8 1.6300 - 1.5600 1.00 3099 132 0.1240 0.1841 REMARK 3 9 1.5600 - 1.5000 1.00 3043 138 0.1351 0.1607 REMARK 3 10 1.5000 - 1.4500 1.00 3064 140 0.1272 0.1867 REMARK 3 11 1.4500 - 1.4000 0.98 3007 128 0.1252 0.1637 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) : 0.112 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.827 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.79 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 1420 REMARK 3 ANGLE : 0.957 1957 REMARK 3 CHIRALITY : 0.062 198 REMARK 3 PLANARITY : 0.010 252 REMARK 3 DIHEDRAL : 14.362 475 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 9KRC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1300053979. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35713 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.14700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M DI-AMMONIUM TARTRATE, 2.2M REMARK 280 AMMONIUM SULFATE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 25.21200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.96950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.72650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.96950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.21200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.72650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 3580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.0 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 ALA A 1 52.09 -146.22 REMARK 500 ALA A 42 46.43 -95.85 REMARK 500 ALA B 1 46.11 -143.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 357 DISTANCE = 5.89 ANGSTROMS 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 HEC A 101 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 18 NE2 REMARK 620 2 HEC A 101 NA 93.0 REMARK 620 3 HEC A 101 NB 89.1 88.9 REMARK 620 4 HEC A 101 NC 83.9 176.9 90.9 REMARK 620 5 HEC A 101 ND 89.6 90.7 178.6 89.5 REMARK 620 6 MET A 58 SD 176.4 83.8 92.4 99.3 88.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC B 101 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 18 NE2 REMARK 620 2 HEC B 101 NA 94.1 REMARK 620 3 HEC B 101 NB 88.4 90.1 REMARK 620 4 HEC B 101 NC 83.0 177.1 89.4 REMARK 620 5 HEC B 101 ND 89.3 91.0 177.5 89.4 REMARK 620 6 MET B 58 SD 176.8 83.0 93.1 99.8 89.2 REMARK 620 N 1 2 3 4 5 DBREF 9KRC A 1 87 UNP P25935 CYC6_SYNE7 25 111 DBREF 9KRC B 1 87 UNP P25935 CYC6_SYNE7 25 111 SEQADV 9KRC GLY A -1 UNP P25935 EXPRESSION TAG SEQADV 9KRC SER A 0 UNP P25935 EXPRESSION TAG SEQADV 9KRC GLY B -1 UNP P25935 EXPRESSION TAG SEQADV 9KRC SER B 0 UNP P25935 EXPRESSION TAG SEQRES 1 A 89 GLY SER ALA ASP LEU ALA HIS GLY GLY GLN VAL PHE SER SEQRES 2 A 89 ALA ASN CYS ALA ALA CYS HIS LEU GLY GLY ARG ASN VAL SEQRES 3 A 89 VAL ASN PRO ALA LYS THR LEU GLN LYS ALA ASP LEU ASP SEQRES 4 A 89 GLN TYR GLY MET ALA SER ILE GLU ALA ILE THR THR GLN SEQRES 5 A 89 VAL THR ASN GLY LYS GLY ALA MET PRO ALA PHE GLY SER SEQRES 6 A 89 LYS LEU SER ALA ASP ASP ILE ALA ASP VAL ALA SER TYR SEQRES 7 A 89 VAL LEU ASP GLN SER GLU LYS GLY TRP GLN GLY SEQRES 1 B 89 GLY SER ALA ASP LEU ALA HIS GLY GLY GLN VAL PHE SER SEQRES 2 B 89 ALA ASN CYS ALA ALA CYS HIS LEU GLY GLY ARG ASN VAL SEQRES 3 B 89 VAL ASN PRO ALA LYS THR LEU GLN LYS ALA ASP LEU ASP SEQRES 4 B 89 GLN TYR GLY MET ALA SER ILE GLU ALA ILE THR THR GLN SEQRES 5 B 89 VAL THR ASN GLY LYS GLY ALA MET PRO ALA PHE GLY SER SEQRES 6 B 89 LYS LEU SER ALA ASP ASP ILE ALA ASP VAL ALA SER TYR SEQRES 7 B 89 VAL LEU ASP GLN SER GLU LYS GLY TRP GLN GLY HET HEC A 101 43 HET SO4 A 102 5 HET HEC B 101 43 HET SO4 B 102 5 HET SO4 B 103 5 HETNAM HEC HEME C HETNAM SO4 SULFATE ION FORMUL 3 HEC 2(C34 H34 FE N4 O4) FORMUL 4 SO4 3(O4 S 2-) FORMUL 8 HOH *313(H2 O) HELIX 1 AA1 ASP A 2 CYS A 14 1 13 HELIX 2 AA2 CYS A 14 LEU A 19 1 6 HELIX 3 AA3 GLY A 20 ARG A 22 5 3 HELIX 4 AA4 GLN A 32 TYR A 39 1 8 HELIX 5 AA5 SER A 43 GLY A 54 1 12 HELIX 6 AA6 SER A 66 GLY A 84 1 19 HELIX 7 AA7 ASP B 2 CYS B 14 1 13 HELIX 8 AA8 CYS B 14 LEU B 19 1 6 HELIX 9 AA9 GLY B 20 ARG B 22 5 3 HELIX 10 AB1 GLN B 32 TYR B 39 1 8 HELIX 11 AB2 SER B 43 GLY B 54 1 12 HELIX 12 AB3 SER B 66 GLY B 84 1 19 LINK SG CYS A 14 CAB HEC A 101 1555 1555 1.77 LINK SG CYS A 17 CAC HEC A 101 1555 1555 1.80 LINK SG CYS B 14 CAB HEC B 101 1555 1555 1.76 LINK SG CYS B 17 CAC HEC B 101 1555 1555 1.79 LINK NE2 HIS A 18 FE HEC A 101 1555 1555 2.01 LINK SD MET A 58 FE HEC A 101 1555 1555 2.38 LINK NE2 HIS B 18 FE HEC B 101 1555 1555 2.03 LINK SD MET B 58 FE HEC B 101 1555 1555 2.37 CRYST1 50.424 53.453 65.939 90.00 90.00 90.00 P 21 21 21 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 0.019832 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018708 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015166 0.00000