HEADER ELECTRON TRANSPORT 02-JUN-11 2YLG TITLE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: ASCORBATE AND CARBON TITLE 2 MONOOXIDE BOUND L16A VARIANT AT 1.05 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C'; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME C PRIME; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACHROMOBACTER XYLOSOXIDANS; SOURCE 3 ORGANISM_TAXID: 85698; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PEC86 KEYWDS ELECTRON TRANSPORT, HAEMOPROTEIN, 4-HELIX BUNDLE EXPDTA X-RAY DIFFRACTION AUTHOR S.V.ANTONYUK,N.RUSTAGE,R.R.EADY,S.S.HASNAIN REVDAT 5 16-OCT-24 2YLG 1 REMARK REVDAT 4 20-DEC-23 2YLG 1 HETSYN REVDAT 3 29-JUL-20 2YLG 1 REMARK SITE REVDAT 2 11-MAR-20 2YLG 1 REMARK SEQRES LINK ATOM REVDAT 1 05-OCT-11 2YLG 0 JRNL AUTH S.V.ANTONYUK,N.RUSTAGE,C.A.PETERSEN,J.L.ARNST,D.J.HEYES, JRNL AUTH 2 R.SHARMA,N.G.BERRY,N.S.SCRUTTON,R.R.EADY,C.R.ANDREW, JRNL AUTH 3 S.S.HASNAIN JRNL TITL CARBON MONOXIDE POISONING IS PREVENTED BY THE ENERGY COSTS JRNL TITL 2 OF CONFORMATIONAL CHANGES IN GAS- BINDING HAEMPROTEINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 15780 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21900609 JRNL DOI 10.1073/PNAS.1109051108 REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 70167 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) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.151 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2924 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) : 1.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5074 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3230 REMARK 3 BIN FREE R VALUE SET COUNT : 211 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 946 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.68000 REMARK 3 B22 (A**2) : -0.68000 REMARK 3 B33 (A**2) : 1.03000 REMARK 3 B12 (A**2) : -0.34000 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): 0.024 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.024 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.020 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.934 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1256 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 736 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1738 ; 2.042 ; 2.078 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1686 ; 1.006 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 172 ; 5.094 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 51 ;31.833 ;24.510 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 198 ;13.190 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;17.908 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 170 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1390 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 199 ; 0.004 ; 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): 766 ; 1.886 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 208 ; 0.646 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1228 ; 2.848 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 490 ; 3.596 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 501 ; 4.938 ; 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): 1992 ; 1.420 ; 3.000 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. U VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 2YLG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1290048517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-09 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 : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73117 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.00 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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: PDB ENTRY 2YL0 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, TRIS PH 7.5. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 120.96200 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 60.48100 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 90.72150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 30.24050 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 151.20250 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 120.96200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 60.48100 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 30.24050 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 90.72150 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 151.20250 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: 5560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.2 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 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 30.24050 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 A2065 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2075 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LEU 16 TO ALA REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 127 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 FE HEC A 128 C CMO A 129 1.82 REMARK 500 O HOH A 2109 O HOH A 2217 2.19 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 2112 O HOH A 2178 8545 2.18 REMARK 500 O HOH A 2069 O HOH A 2109 5555 2.18 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 ASP A 37 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 CYS A 116 CA - CB - SG ANGL. DEV. = 7.1 DEGREES 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 A2014 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A2034 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A2043 DISTANCE = 6.88 ANGSTROMS REMARK 525 HOH A2067 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH A2068 DISTANCE = 6.98 ANGSTROMS REMARK 525 HOH A2077 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A2078 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A2106 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A2135 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A2166 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A2173 DISTANCE = 6.99 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 128 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HEC A 128 NA 89.0 REMARK 620 3 HEC A 128 NB 88.2 91.3 REMARK 620 4 HEC A 128 NC 87.4 176.2 89.8 REMARK 620 5 HEC A 128 ND 90.0 88.4 178.2 90.4 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YL3 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE REMARK 900 BOUND L16G VARIANT AT 1.04 A RESOLUTION REMARK 900 RELATED ID: 2XLH RELATED DB: PDB REMARK 900 REDUCED STRUCTURE OF R124A MUTANT OF CYTOCHROME C' FROM ALCALIGENES REMARK 900 XYLOSOXIDANS REMARK 900 RELATED ID: 2XM0 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124K REMARK 900 VARIANT REMARK 900 RELATED ID: 1CGO RELATED DB: PDB REMARK 900 CYTOCHROME C' REMARK 900 RELATED ID: 2YKZ RELATED DB: PDB REMARK 900 RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS REMARK 900 AT 0.84 A RESOLUTION: RESTRAINED REFINEMENT REMARK 900 RELATED ID: 2XM4 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124E REMARK 900 VARIANT REMARK 900 RELATED ID: 1E86 RELATED DB: PDB REMARK 900 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE REMARK 900 WITH CO BOUND TO DISTAL SIDE OF HEME REMARK 900 RELATED ID: 2XL6 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124A REMARK 900 VARIANT WITH BOUND NO REMARK 900 RELATED ID: 2YL0 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: AS ISOLATED L16A REMARK 900 VARIANT AT 0.95 A RESOLUTION REMARK 900 RELATED ID: 1E85 RELATED DB: PDB REMARK 900 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE REMARK 900 WITH NO BOUND TO PROXIMAL SIDE OF HEME REMARK 900 RELATED ID: 1CGN RELATED DB: PDB REMARK 900 CYTOCHROME C' REMARK 900 RELATED ID: 2XLM RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS REMARK 900 RECOMBINANT NATIVE WITH BOUND NO REMARK 900 RELATED ID: 2YL1 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE REMARK 900 BOUND L16A VARIANT AT 1.03 A RESOLUTION REMARK 900 RELATED ID: 2XLD RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124Q REMARK 900 VARIANT REMARK 900 RELATED ID: 2XLE RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124K REMARK 900 VARIANT WITH BOUND NO REMARK 900 RELATED ID: 1E83 RELATED DB: PDB REMARK 900 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - OXIDIZED STRUCTURE REMARK 900 RELATED ID: 2YL7 RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: AS ISOLATED L16G REMARK 900 VARIANT AT 0.9 A RESOLUTION REMARK 900 RELATED ID: 2XL8 RELATED DB: PDB REMARK 900 REDUCED STRUCTURE OF R124F MUTANT OF CYTOCHROME C' FROM ALCALIGENES REMARK 900 XYLOSOXIDANS REMARK 900 RELATED ID: 2XLW RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124Q REMARK 900 VARIANT WITH BOUND NO REMARK 900 RELATED ID: 1E84 RELATED DB: PDB REMARK 900 CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE REMARK 900 RELATED ID: 2XLV RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124F REMARK 900 VARIANT WITH BOUND NO REMARK 900 RELATED ID: 2XLO RELATED DB: PDB REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124E REMARK 900 VARIANT WITH BOUND NO REMARK 900 RELATED ID: 2YLI RELATED DB: PDB REMARK 900 RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS REMARK 900 IN ITS FERROUS FORM AT 1.45 A DBREF 2YLG A 1 127 UNP P00138 CYCP_ALCXX 1 127 SEQADV 2YLG ALA A 16 UNP P00138 LEU 16 ENGINEERED MUTATION SEQRES 1 A 127 PCA PHE ALA LYS PRO GLU ASP ALA VAL LYS TYR ARG GLN SEQRES 2 A 127 SER ALA ALA THR LEU MET ALA SER HIS PHE GLY ARG MET SEQRES 3 A 127 THR PRO VAL VAL LYS GLY GLN ALA PRO TYR ASP ALA ALA SEQRES 4 A 127 GLN ILE LYS ALA ASN VAL GLU VAL LEU LYS THR LEU SER SEQRES 5 A 127 ALA LEU PRO TRP ALA ALA PHE GLY PRO GLY THR GLU GLY SEQRES 6 A 127 GLY ASP ALA ARG PRO GLU ILE TRP SER ASP ALA ALA SER SEQRES 7 A 127 PHE LYS GLN LYS GLN GLN ALA PHE GLN ASP ASN ILE VAL SEQRES 8 A 127 LYS LEU SER ALA ALA ALA ASP ALA GLY ASP LEU ASP LYS SEQRES 9 A 127 LEU ARG ALA ALA PHE GLY ASP VAL GLY ALA SER CYS LYS SEQRES 10 A 127 ALA CYS HIS ASP ALA TYR ARG LYS LYS LYS MODRES 2YLG PCA A 1 GLU PYROGLUTAMIC ACID HET PCA A 1 15 HET HEC A 128 75 HET CMO A 129 2 HET ASC A 130 20 HET SO4 A 131 5 HET SO4 A 132 5 HETNAM PCA PYROGLUTAMIC ACID HETNAM HEC HEME C HETNAM CMO CARBON MONOXIDE HETNAM ASC ASCORBIC ACID HETNAM SO4 SULFATE ION HETSYN ASC VITAMIN C FORMUL 1 PCA C5 H7 N O3 FORMUL 2 HEC C34 H34 FE N4 O4 FORMUL 3 CMO C O FORMUL 4 ASC C6 H8 O6 FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 HOH *320(H2 O) HELIX 1 1 LYS A 4 ARG A 25 1 22 HELIX 2 2 MET A 26 LYS A 31 1 6 HELIX 3 3 ASP A 37 ALA A 53 1 17 HELIX 4 4 LEU A 54 PHE A 59 5 6 HELIX 5 5 PRO A 70 ASP A 75 1 6 HELIX 6 6 ASP A 75 GLY A 100 1 26 HELIX 7 7 ASP A 101 ARG A 124 1 24 LINK C PCA A 1 N PHE A 2 1555 1555 1.34 LINK SG CYS A 116 CAB HEC A 128 1555 1555 1.86 LINK SG CYS A 119 CAC HEC A 128 1555 1555 1.90 LINK NE2 HIS A 120 FE HEC A 128 1555 1555 2.08 CRYST1 53.640 53.640 181.443 90.00 90.00 120.00 P 65 2 2 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 0.018643 0.010763 0.000000 0.00000 SCALE2 0.000000 0.021527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005511 0.00000 HETATM 1 N PCA A 1 29.844 -7.313 2.019 1.00 13.87 N ANISOU 1 N PCA A 1 2474 2197 597 259 298 270 N HETATM 2 CA PCA A 1 30.431 -6.801 3.225 1.00 14.43 C ANISOU 2 CA PCA A 1 2540 2256 685 256 377 257 C HETATM 3 CB PCA A 1 29.318 -6.975 4.254 1.00 15.24 C ANISOU 3 CB PCA A 1 2753 2383 655 321 399 124 C HETATM 4 CG PCA A 1 28.503 -8.124 3.740 1.00 14.83 C ANISOU 4 CG PCA A 1 2644 2283 707 236 607 401 C HETATM 5 CD PCA A 1 28.785 -8.148 2.282 1.00 14.76 C ANISOU 5 CD PCA A 1 2567 2224 814 152 66 318 C HETATM 6 OE PCA A 1 28.201 -8.820 1.439 1.00 16.26 O ANISOU 6 OE PCA A 1 2762 2549 865 35 300 417 O HETATM 7 C PCA A 1 31.691 -7.534 3.634 1.00 14.34 C ANISOU 7 C PCA A 1 2462 2303 681 192 228 204 C HETATM 8 O PCA A 1 32.159 -7.304 4.751 1.00 16.34 O ANISOU 8 O PCA A 1 2832 2709 666 48 157 76 O HETATM 9 H PCA A 1 30.487 -7.372 1.311 1.00 13.97 H ANISOU 9 H PCA A 1 2448 2185 672 257 316 262 H HETATM 10 HA PCA A 1 30.619 -5.843 3.133 1.00 14.39 H ANISOU 10 HA PCA A 1 2538 2241 687 275 358 226 H HETATM 11 HB2 PCA A 1 28.821 -6.135 4.342 1.00 14.67 H ANISOU 11 HB2 PCA A 1 2564 2288 721 256 380 224 H HETATM 12 HB3 PCA A 1 29.688 -7.201 5.132 1.00 14.67 H ANISOU 12 HB3 PCA A 1 2559 2267 746 270 398 242 H HETATM 13 HG2 PCA A 1 27.564 -8.000 3.993 1.00 14.72 H ANISOU 13 HG2 PCA A 1 2578 2257 756 246 501 321 H HETATM 14 HG3 PCA A 1 28.819 -8.955 4.150 1.00 14.75 H ANISOU 14 HG3 PCA A 1 2599 2229 776 228 439 313 H HETATM 15 HN2 PCA A 1 29.523 -6.413 2.053 1.00 13.89 H ANISOU 15 HN2 PCA A 1 2446 2164 665 241 268 270 H