HEADER ELECTRON TRANSPORT 23-NOV-22 8BRK TITLE ROOM TEMPERATURE CRYSTAL STRUCTURE OF CYTOCHROME C' FROM THERMUS TITLE 2 THERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE CYTOCHROME; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 GENE: TT_P0091; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEME PROTEIN, DIATOMIC GAS BINDING PROTEIN, ELECTRON TRANSFER, KEYWDS 2 ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.FUJII,M.A.HOUGH REVDAT 4 07-FEB-24 8BRK 1 REMARK REVDAT 3 19-JUL-23 8BRK 1 JRNL REMARK REVDAT 2 31-MAY-23 8BRK 1 JRNL REVDAT 1 24-MAY-23 8BRK 0 JRNL AUTH H.MIKOLAJEK,J.SANCHEZ-WEATHERBY,J.SANDY,R.J.GILDEA, JRNL AUTH 2 I.CAMPEOTTO,H.CHERUVARA,J.D.CLARKE,T.FOSTER,S.FUJII, JRNL AUTH 3 I.T.PAULSEN,B.S.SHAH,M.A.HOUGH JRNL TITL PROTEIN-TO-STRUCTURE PIPELINE FOR AMBIENT-TEMPERATURE IN JRNL TITL 2 SITU CRYSTALLOGRAPHY AT VMXI. JRNL REF IUCRJ V. 10 420 2023 JRNL REFN ESSN 2052-2525 JRNL PMID 37199504 JRNL DOI 10.1107/S2052252523003810 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 11811 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 614 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 709 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE SET COUNT : 39 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1058 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.76000 REMARK 3 B22 (A**2) : -0.52000 REMARK 3 B33 (A**2) : 1.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.07000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.117 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.523 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1149 ; 0.012 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1042 ; 0.001 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1579 ; 2.229 ; 1.737 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2415 ; 1.320 ; 1.621 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 134 ; 6.957 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 51 ;26.304 ;21.373 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 164 ;15.183 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;21.208 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 130 ; 0.144 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1298 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 260 ; 0.013 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 539 ; 1.880 ; 2.294 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 538 ; 1.872 ; 2.293 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 672 ; 2.907 ; 3.436 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 673 ; 2.906 ; 3.437 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 610 ; 2.718 ; 2.546 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 608 ; 2.722 ; 2.550 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 907 ; 4.387 ; 3.677 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1314 ; 5.419 ;26.089 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1303 ; 5.364 ;25.897 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8BRK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : VMXI REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7749 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : XIA2.MULTIPLEX REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12429 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 35.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.15100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.17100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 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: 7EAD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7, 0.2 M SODIUM REMARK 280 CHLORIDE, 20% (W/V) PEG 6000, PH 7.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.76750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.49300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.76750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.49300 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: 4750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 ASN A 71 47.04 -109.67 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 HEC A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HEC A 201 NA 90.9 REMARK 620 3 HEC A 201 NB 95.6 88.4 REMARK 620 4 HEC A 201 NC 95.9 173.0 89.5 REMARK 620 5 HEC A 201 ND 93.5 92.1 170.9 88.9 REMARK 620 N 1 2 3 4 DBREF 8BRK A 1 135 UNP Q746G4 Q746G4_THET2 20 154 SEQRES 1 A 135 GLY LEU PRO TYR PRO GLU GLY TYR ARG PHE TRP THR HIS SEQRES 2 A 135 VAL LYS SER MET GLU LEU LYS PRO GLY HIS PRO LEU TYR SEQRES 3 A 135 GLU SER PHE GLY GLY LEU HIS HIS ILE TYR VAL ASN PRO SEQRES 4 A 135 THR GLY LEU ARG THR TYR LEU GLU GLY LYS LYS ALA PRO SEQRES 5 A 135 PHE PRO LYS GLY THR VAL ILE VAL PHE ASP LEU LEU GLU SEQRES 6 A 135 ALA LYS VAL GLU GLY ASN ALA LEU LEU GLU GLY PRO ARG SEQRES 7 A 135 LYS LEU ILE GLY VAL MET ALA LYS ASP PRO GLY ARG TYR SEQRES 8 A 135 PRO ASP THR GLY GLY TRP GLY TYR TYR ALA PHE GLY PRO SEQRES 9 A 135 ASP LYS LYS PRO LEU ALA ILE ASP PRO LYS ALA CYS HIS SEQRES 10 A 135 ALA CYS HIS GLN GLY ALA ALA ASN THR ASP TYR VAL PHE SEQRES 11 A 135 SER ALA PHE ARG PRO HET HEC A 201 43 HETNAM HEC HEME C FORMUL 2 HEC C34 H34 FE N4 O4 FORMUL 3 HOH *75(H2 O) HELIX 1 AA1 GLY A 7 TRP A 11 5 5 HELIX 2 AA2 LEU A 25 GLY A 30 1 6 HELIX 3 AA3 ASN A 38 GLU A 47 1 10 HELIX 4 AA4 TYR A 91 GLY A 95 5 5 HELIX 5 AA5 ASP A 112 GLN A 121 1 10 HELIX 6 AA6 GLY A 122 ASP A 127 5 6 SHEET 1 AA1 5 THR A 12 LEU A 19 0 SHEET 2 AA1 5 GLY A 31 VAL A 37 -1 O ILE A 35 N VAL A 14 SHEET 3 AA1 5 VAL A 58 GLU A 69 -1 O ASP A 62 N HIS A 34 SHEET 4 AA1 5 ALA A 72 LYS A 86 -1 O LYS A 79 N LEU A 63 SHEET 5 AA1 5 TRP A 97 PHE A 102 -1 O TYR A 100 N VAL A 83 LINK SG CYS A 116 CAB HEC A 201 1555 1555 1.75 LINK SG CYS A 119 CAC HEC A 201 1555 1555 1.87 LINK NE2 HIS A 120 FE HEC A 201 1555 1555 2.17 CRYST1 81.535 38.986 41.525 90.00 97.24 90.00 C 1 2 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 0.012265 0.000000 0.001558 0.00000 SCALE2 0.000000 0.025650 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024275 0.00000