HEADER ELECTRON TRANSPORT 10-JAN-25 9MT0 TITLE 1.2 A CRYSTAL STRUCTURE OF HOUSEFLY CYTOCHROME C AT PH 11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUSCA DOMESTICA; SOURCE 3 ORGANISM_COMMON: HOUSE FLY; SOURCE 4 ORGANISM_TAXID: 7370; SOURCE 5 ORGAN: THORAX; SOURCE 6 TISSUE: FLIGHT MUSCLE KEYWDS ELECTRON TRANSPORT, METALLOPROTEINS, INSECT, PROTOSTOME, CYTOCHROME KEYWDS 2 C, ALKALINE PH EXPDTA X-RAY DIFFRACTION AUTHOR L.ZAFREEN,L.-S.HUANG,P.LUEMMEN,E.A.BERRY REVDAT 1 12-FEB-25 9MT0 0 JRNL AUTH L.ZAFREEN,L.-S.HUANG,P.LUEMMEN,E.A.BERRY JRNL TITL CRYSTAL STRUCTURE OF INSECT CYTOCHROME C AT DIFFERENT PH JRNL TITL 2 VALUES. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3150 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.930 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 3 NUMBER OF REFLECTIONS : 55798 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.127 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1574 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 37.8000 - 2.6700 0.95 5149 154 0.1275 0.1537 REMARK 3 2 2.6700 - 2.1200 1.00 5331 157 0.1191 0.1564 REMARK 3 3 2.1200 - 1.8500 1.00 5354 156 0.1110 0.1607 REMARK 3 4 1.8500 - 1.6800 0.99 5287 151 0.1030 0.1572 REMARK 3 5 1.6800 - 1.5600 0.99 5304 161 0.1049 0.1420 REMARK 3 6 1.5600 - 1.4700 0.99 5198 151 0.1132 0.1498 REMARK 3 7 1.4700 - 1.4000 0.98 5230 148 0.1283 0.2051 REMARK 3 8 1.4000 - 1.3300 0.98 5220 148 0.1771 0.2301 REMARK 3 9 1.3300 - 1.2800 0.96 5120 159 0.2062 0.2249 REMARK 3 10 1.2800 - 1.2400 0.84 4450 119 0.2286 0.2830 REMARK 3 11 1.2400 - 1.2000 0.48 2581 70 0.2793 0.3019 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) : 0.126 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.338 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.76 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 : 0.009 1907 REMARK 3 ANGLE : 1.105 2604 REMARK 3 CHIRALITY : 0.074 253 REMARK 3 PLANARITY : 0.013 333 REMARK 3 DIHEDRAL : 13.757 710 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 9MT0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000291110. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9804 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55990 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 38.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 5.360 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 45.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.41 REMARK 200 R MERGE FOR SHELL (I) : 0.45900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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 (%): 41.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CONCENTRATED PROTEIN IN 0.5 MM EDTA, REMARK 280 20 MM TRIS-HCL PH 7.5 WAS MIXED WITH AN EQUAL VOLUME OF REMARK 280 PRECIPITANT CONTAINING 0.1 M GLYCINE PH 10.0 AND 28% W/V REMARK 280 POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000 AND ALLOWED TO VAPOR REMARK 280 DIFFUSE AGAINST A RESERVOIR OF THE SAME PRECIPITANT. BEFORE REMARK 280 CRYOPROTECTION AND FREEZING, THE CRYSTAL WAS TRANSFERRED TO A REMARK 280 WELL CONTAINING 0.1 M CAPS PH 11.0 AND 28% W/V POLYETHYLENE REMARK 280 GLYCOL MONOMETHYL ETHER 2000. THE CRYSTAL FRACTURED, AND A REMARK 280 FRAGMENT WAS UED FOR COLLECTION., PH 9.7, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.31700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 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 O HOH A 356 O HOH A 424 2.09 REMARK 500 O LYS B 103 O HOH B 301 2.18 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 27 -139.74 -125.43 REMARK 500 ASN A 70 86.90 -165.37 REMARK 500 LYS B 27 -135.12 -123.03 REMARK 500 ASN B 70 84.50 -159.54 REMARK 500 ASN B 70 84.50 -166.24 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 B 448 DISTANCE = 5.84 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 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 18 NE2 REMARK 620 2 HEC A 201 NA 90.1 REMARK 620 3 HEC A 201 NB 89.0 92.0 REMARK 620 4 HEC A 201 NC 91.1 178.8 88.1 REMARK 620 5 HEC A 201 ND 91.2 87.6 179.6 92.2 REMARK 620 6 MET A 80 SD 173.6 83.5 91.0 95.3 88.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC B 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 18 NE2 REMARK 620 2 HEC B 201 NA 91.3 REMARK 620 3 HEC B 201 NB 86.3 89.6 REMARK 620 4 HEC B 201 NC 91.6 177.1 90.3 REMARK 620 5 HEC B 201 ND 91.3 89.7 177.5 90.5 REMARK 620 6 MET B 80 SD 176.6 85.4 94.5 91.7 87.8 REMARK 620 N 1 2 3 4 5 DBREF1 9MT0 A -3 103 UNP A0A1I8N8V4_MUSDO DBREF2 9MT0 A A0A1I8N8V4 2 108 DBREF1 9MT0 B -3 103 UNP A0A1I8N8V4_MUSDO DBREF2 9MT0 B A0A1I8N8V4 2 108 SEQRES 1 A 107 GLY VAL PRO ALA GLY ASP VAL GLU LYS GLY LYS LYS ILE SEQRES 2 A 107 PHE VAL GLN ARG CYS ALA GLN CYS HIS THR VAL GLU ALA SEQRES 3 A 107 GLY GLY LYS HIS LYS VAL GLY PRO ASN LEU HIS GLY LEU SEQRES 4 A 107 PHE GLY ARG LYS THR GLY GLN ALA ALA GLY PHE ALA TYR SEQRES 5 A 107 THR ASP ALA ASN LYS ALA LYS GLY ILE THR TRP ASN GLU SEQRES 6 A 107 ASP THR LEU PHE GLU TYR LEU GLU ASN PRO LYS LYS TYR SEQRES 7 A 107 ILE PRO GLY THR LYS MET ILE PHE ALA GLY LEU LYS LYS SEQRES 8 A 107 PRO ASN GLU ARG GLY ASP LEU ILE ALA TYR LEU LYS SER SEQRES 9 A 107 ALA THR LYS SEQRES 1 B 107 GLY VAL PRO ALA GLY ASP VAL GLU LYS GLY LYS LYS ILE SEQRES 2 B 107 PHE VAL GLN ARG CYS ALA GLN CYS HIS THR VAL GLU ALA SEQRES 3 B 107 GLY GLY LYS HIS LYS VAL GLY PRO ASN LEU HIS GLY LEU SEQRES 4 B 107 PHE GLY ARG LYS THR GLY GLN ALA ALA GLY PHE ALA TYR SEQRES 5 B 107 THR ASP ALA ASN LYS ALA LYS GLY ILE THR TRP ASN GLU SEQRES 6 B 107 ASP THR LEU PHE GLU TYR LEU GLU ASN PRO LYS LYS TYR SEQRES 7 B 107 ILE PRO GLY THR LYS MET ILE PHE ALA GLY LEU LYS LYS SEQRES 8 B 107 PRO ASN GLU ARG GLY ASP LEU ILE ALA TYR LEU LYS SER SEQRES 9 B 107 ALA THR LYS HET HEC A 201 75 HET EOH A 202 9 HET HEC B 201 75 HETNAM HEC HEME C HETNAM EOH ETHANOL FORMUL 3 HEC 2(C34 H34 FE N4 O4) FORMUL 4 EOH C2 H6 O FORMUL 6 HOH *303(H2 O) HELIX 1 AA1 ASP A 2 CYS A 14 1 13 HELIX 2 AA2 THR A 49 GLY A 56 1 8 HELIX 3 AA3 ASN A 60 ASN A 70 1 11 HELIX 4 AA4 ASN A 70 ILE A 75 1 6 HELIX 5 AA5 LYS A 87 THR A 102 1 16 HELIX 6 AA6 ASP B 2 CYS B 14 1 13 HELIX 7 AA7 THR B 49 GLY B 56 1 8 HELIX 8 AA8 ASN B 60 ASN B 70 1 11 HELIX 9 AA9 ASN B 70 ILE B 75 1 6 HELIX 10 AB1 LYS B 87 THR B 102 1 16 LINK SG CYS A 14 CAB HEC A 201 1555 1555 1.76 LINK SG CYS A 17 CAC HEC A 201 1555 1555 1.81 LINK SG CYS B 14 CAB HEC B 201 1555 1555 1.76 LINK SG CYS B 17 CAC HEC B 201 1555 1555 1.87 LINK NE2 HIS A 18 FE HEC A 201 1555 1555 2.03 LINK SD MET A 80 FE HEC A 201 1555 1555 2.28 LINK NE2 HIS B 18 FE HEC B 201 1555 1555 2.00 LINK SD MET B 80 FE HEC B 201 1555 1555 2.28 CRYST1 33.876 58.634 51.674 90.00 106.77 90.00 P 1 21 1 4 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 0.029519 0.000000 0.008897 0.00000 SCALE2 0.000000 0.017055 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020212 0.00000