HEADER ELECTRON TRANSPORT 30-OCT-06 2J8W TITLE THE CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RUBRIVIVAX GELATINOSUS AT TITLE 2 1.3 A RESOLUTION AND PH 8.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C'; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RUBRIVIVAX GELATINOSUS; SOURCE 3 ORGANISM_TAXID: 28068; SOURCE 4 STRAIN: DSM 1709; SOURCE 5 OTHER_DETAILS: DSMZ KEYWDS C', HEME, IRON, TRANSPORT, CYTOCHROME, METAL-BINDING, ELECTRON KEYWDS 2 TRANSFER, ELECTRON TRANSPORT, RUBRIVIVAX GELATINOSUS EXPDTA X-RAY DIFFRACTION AUTHOR S.BENINI,S.CIURLI,W.R.RYPNIEWSKI,K.S.WILSON REVDAT 9 13-DEC-23 2J8W 1 LINK REVDAT 8 24-JUL-19 2J8W 1 REMARK REVDAT 7 10-JUL-19 2J8W 1 REMARK REVDAT 6 08-MAY-19 2J8W 1 REMARK LINK REVDAT 5 23-JAN-19 2J8W 1 COMPND JRNL REMARK HET REVDAT 5 2 1 HETNAM HETSYN FORMUL LINK REVDAT 5 3 1 ATOM REVDAT 4 24-FEB-09 2J8W 1 VERSN REVDAT 3 29-APR-08 2J8W 1 KEYWDS JRNL MASTER REVDAT 2 15-APR-08 2J8W 1 REMARK ATOM ANISOU HETATM REVDAT 2 2 1 CONECT MASTER REVDAT 1 06-NOV-07 2J8W 0 JRNL AUTH S.BENINI,W.R.RYPNIEWSKI,K.S.WILSON,S.CIURLI JRNL TITL HIGH RESOLUTION CRYSTAL STRUCTURE OF RUBRIVIVAX GELATINOSUS JRNL TITL 2 CYTOCHROME C'. JRNL REF J. INORG. BIOCHEM. V. 102 1322 2008 JRNL REFN ISSN 0162-0134 JRNL PMID 18295896 JRNL DOI 10.1016/J.JINORGBIO.2008.01.017 REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 85947 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) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1755 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) : 1.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.32 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6167 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1830 REMARK 3 BIN FREE R VALUE SET COUNT : 128 REMARK 3 BIN FREE R VALUE : 0.2130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1804 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 545 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.64000 REMARK 3 B22 (A**2) : 0.64000 REMARK 3 B33 (A**2) : -0.96000 REMARK 3 B12 (A**2) : 0.32000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.039 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.022 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.139 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2015 ; 0.016 ; 0.025 REMARK 3 BOND LENGTHS OTHERS (A): 1272 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2760 ; 1.744 ; 2.104 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3113 ; 1.019 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 262 ; 4.577 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 75 ;35.434 ;25.067 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 274 ;11.422 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;16.650 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 284 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2336 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 390 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 514 ; 0.293 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1284 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1018 ; 0.192 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 892 ; 0.092 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 334 ; 0.181 ; 0.200 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): 4 ; 0.157 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 22 ; 0.199 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.195 ; 0.200 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): 1368 ; 1.967 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2023 ; 2.395 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 798 ; 3.470 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 733 ; 4.527 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.40 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 2J8W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1290030284. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9077 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 87744 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 19.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.48 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.580 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1JAF REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP 2.5 M AMMONIUM SULPHATE REMARK 280 0.1M TRIS-HCL PH8.0, VAPOR DIFFUSION, HANGING DROP 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 41.21000 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 82.42000 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 82.42000 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 41.21000 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.4 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B2247 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 1 CG CD OE1 NE2 REMARK 470 GLN A 3 CG CD OE1 NE2 REMARK 470 LYS A 4 CD CE NZ REMARK 470 LYS A 65 CB CG CD CE NZ REMARK 470 LYS A 72 CE NZ REMARK 470 LYS A 120 CD CE NZ REMARK 470 LYS A 125 CG CD CE NZ REMARK 470 GLU A 128 CD OE1 OE2 REMARK 470 LYS A 129 CA C O CB CG CD CE REMARK 470 LYS A 129 NZ REMARK 470 GLN B 1 CB CG CD OE1 NE2 REMARK 470 GLN B 3 CD OE1 NE2 REMARK 470 LYS B 4 CG CD CE NZ REMARK 470 LYS B 65 CD CE NZ REMARK 470 LYS B 72 CE NZ REMARK 470 LYS B 95 NZ REMARK 470 LYS B 120 CD CE NZ REMARK 470 LYS B 125 CD CE NZ REMARK 470 LYS B 129 CA C O CB CG CD CE REMARK 470 LYS B 129 NZ 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 OD1 ASP B 97 O HOH B 2235 1.61 REMARK 500 CE LYS B 95 O HOH B 2225 1.95 REMARK 500 O HOH B 2224 O HOH B 2225 1.98 REMARK 500 O HOH A 2059 O HOH A 2147 2.05 REMARK 500 O TRP A 76 O HOH A 2179 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2037 O HOH B 2126 4656 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS B 101 CD - CE - NZ ANGL. DEV. = -14.8 DEGREES 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 THR A 63 31.40 -99.81 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 A2004 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A2008 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A2013 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2031 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A2034 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A2042 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH B2010 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH B2016 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH B2017 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH B2053 DISTANCE = 6.72 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 A1129 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 123 NE2 REMARK 620 2 HEC A1129 NA 98.1 REMARK 620 3 HEC A1129 NB 95.8 90.7 REMARK 620 4 HEC A1129 NC 95.5 166.4 88.1 REMARK 620 5 HEC A1129 ND 97.5 89.0 166.6 89.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC B1129 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 123 NE2 REMARK 620 2 HEC B1129 NA 97.6 REMARK 620 3 HEC B1129 NB 96.4 89.4 REMARK 620 4 HEC B1129 NC 96.0 166.4 90.3 REMARK 620 5 HEC B1129 ND 97.7 89.6 165.9 87.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A1129 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B1129 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JAF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CYTOCHROME C' FROM RHODOCYCLUS GELATINOSUS AT REMARK 900 2.5 ANGSTOMS RESOLUTION REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE LAST K OF THE ORIGINAL SEQUENCE (P00142) IS NOT REMARK 999 PRESENT IN THE MODEL DBREF 2J8W A 1 129 UNP P00142 CYCP_RHOGE 1 129 DBREF 2J8W B 1 129 UNP P00142 CYCP_RHOGE 1 129 SEQRES 1 A 129 GLN PHE GLN LYS PRO GLY ASP ALA ILE GLU TYR ARG GLN SEQRES 2 A 129 SER ALA PHE THR LEU ILE ALA ASN HIS PHE GLY ARG VAL SEQRES 3 A 129 ALA ALA MET ALA GLN GLY LYS ALA PRO PHE ASP ALA LYS SEQRES 4 A 129 VAL ALA ALA GLU ASN ILE ALA LEU VAL SER THR LEU SER SEQRES 5 A 129 LYS LEU PRO LEU THR ALA PHE GLY PRO GLY THR ASP LYS SEQRES 6 A 129 GLY HIS GLY THR GLU ALA LYS PRO ALA VAL TRP SER ASP SEQRES 7 A 129 ALA ALA GLY PHE LYS ALA ALA ALA ASP LYS PHE ALA ALA SEQRES 8 A 129 ALA VAL ASP LYS LEU ASP ALA ALA GLY LYS THR GLY ASP SEQRES 9 A 129 PHE ALA GLN ILE LYS ALA ALA VAL GLY GLU THR GLY GLY SEQRES 10 A 129 ALA CYS LYS GLY CYS HIS ASP LYS PHE LYS GLU LYS SEQRES 1 B 129 GLN PHE GLN LYS PRO GLY ASP ALA ILE GLU TYR ARG GLN SEQRES 2 B 129 SER ALA PHE THR LEU ILE ALA ASN HIS PHE GLY ARG VAL SEQRES 3 B 129 ALA ALA MET ALA GLN GLY LYS ALA PRO PHE ASP ALA LYS SEQRES 4 B 129 VAL ALA ALA GLU ASN ILE ALA LEU VAL SER THR LEU SER SEQRES 5 B 129 LYS LEU PRO LEU THR ALA PHE GLY PRO GLY THR ASP LYS SEQRES 6 B 129 GLY HIS GLY THR GLU ALA LYS PRO ALA VAL TRP SER ASP SEQRES 7 B 129 ALA ALA GLY PHE LYS ALA ALA ALA ASP LYS PHE ALA ALA SEQRES 8 B 129 ALA VAL ASP LYS LEU ASP ALA ALA GLY LYS THR GLY ASP SEQRES 9 B 129 PHE ALA GLN ILE LYS ALA ALA VAL GLY GLU THR GLY GLY SEQRES 10 B 129 ALA CYS LYS GLY CYS HIS ASP LYS PHE LYS GLU LYS HET HEC A1129 46 HET HEC B1129 46 HETNAM HEC HEME C FORMUL 3 HEC 2(C34 H34 FE N4 O4) FORMUL 5 HOH *545(H2 O) HELIX 1 1 LYS A 4 GLN A 31 1 28 HELIX 2 2 ASP A 37 LYS A 53 1 17 HELIX 3 3 LEU A 54 ALA A 58 5 5 HELIX 4 4 PRO A 73 ASP A 78 1 6 HELIX 5 5 ASP A 78 GLY A 103 1 26 HELIX 6 6 ASP A 104 LYS A 127 1 24 HELIX 7 7 LYS B 4 GLN B 31 1 28 HELIX 8 8 ASP B 37 LYS B 53 1 17 HELIX 9 9 LEU B 54 ALA B 58 5 5 HELIX 10 10 PRO B 73 ASP B 78 1 6 HELIX 11 11 ASP B 78 GLY B 103 1 26 HELIX 12 12 ASP B 104 LYS B 127 1 24 LINK SG CYS A 119 CAB HEC A1129 1555 1555 1.89 LINK SG CYS A 122 CAC HEC A1129 1555 1555 1.95 LINK SG CYS B 119 CAB HEC B1129 1555 1555 1.88 LINK SG CYS B 122 CAC HEC B1129 1555 1555 1.92 LINK NE2 HIS A 123 FE HEC A1129 1555 1555 2.16 LINK NE2 HIS B 123 FE HEC B1129 1555 1555 2.11 SITE 1 AC1 22 ARG A 12 GLN A 13 PHE A 16 THR A 17 SITE 2 AC1 22 ILE A 19 PHE A 59 THR A 69 GLU A 70 SITE 3 AC1 22 PHE A 82 ALA A 86 PHE A 89 CYS A 119 SITE 4 AC1 22 CYS A 122 HIS A 123 LYS A 127 HOH A2174 SITE 5 AC1 22 HOH A2255 HOH A2256 HOH A2257 HOH A2258 SITE 6 AC1 22 HOH A2259 HOH A2260 SITE 1 AC2 20 ARG B 12 GLN B 13 PHE B 16 THR B 17 SITE 2 AC2 20 ILE B 19 THR B 69 GLU B 70 PHE B 82 SITE 3 AC2 20 ALA B 85 ALA B 86 PHE B 89 CYS B 119 SITE 4 AC2 20 CYS B 122 HIS B 123 LYS B 127 HOH B2189 SITE 5 AC2 20 HOH B2190 HOH B2283 HOH B2284 HOH B2285 CRYST1 69.630 69.630 123.630 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 0.014362 0.008292 0.000000 0.00000 SCALE2 0.000000 0.016583 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008089 0.00000