HEADER ELECTRON TRANSPORT 02-JUN-11 2YLD
TITLE RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS:
TITLE 2 CARBON MONOOXIDE BOUND AT 1.25 A
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CYTOCHROME C';
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: CYTOCHROME C PRIME;
COMPND 5 ENGINEERED: 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 4 20-DEC-23 2YLD 1 HETSYN
REVDAT 3 29-JUL-20 2YLD 1 REMARK SITE
REVDAT 2 11-MAR-20 2YLD 1 REMARK SEQRES LINK ATOM
REVDAT 1 05-OCT-11 2YLD 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. 1.25 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) : 1.25
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.68
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6
REMARK 3 NUMBER OF REFLECTIONS : 40961
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) : 0.163
REMARK 3 R VALUE (WORKING SET) : 0.161
REMARK 3 FREE R VALUE : 0.190
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2172
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) : 1.25
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2420
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.83
REMARK 3 BIN R VALUE (WORKING SET) : 0.3250
REMARK 3 BIN FREE R VALUE SET COUNT : 125
REMARK 3 BIN FREE R VALUE : 0.3640
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 949
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 67
REMARK 3 SOLVENT ATOMS : 253
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 11.90
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.46
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.54000
REMARK 3 B22 (A**2) : -0.54000
REMARK 3 B33 (A**2) : 0.81000
REMARK 3 B12 (A**2) : -0.27000
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): 0.045
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.045
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.563
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1156 ; 0.019 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 815 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1597 ; 2.090 ; 2.104
REMARK 3 BOND ANGLES OTHERS (DEGREES): 1865 ; 0.954 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 154 ; 4.634 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 49 ;32.113 ;24.490
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 195 ;14.667 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;25.427 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 160 ; 0.127 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1324 ; 0.009 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 217 ; 0.001 ; 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): 678 ; 2.289 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 241 ; 0.696 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1087 ; 3.247 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 478 ; 4.215 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 495 ; 6.219 ; 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): 1971 ; 1.479 ; 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 : 1.40
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.U VALUES REFINED INDIVIDUALLY.
REMARK 4
REMARK 4 2YLD 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_1290048522.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-SEP-08
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 : SRS
REMARK 200 BEAMLINE : PX10.1
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 : SI(111)
REMARK 200 OPTICS : MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40961
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250
REMARK 200 RESOLUTION RANGE LOW (A) : 36.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8
REMARK 200 DATA REDUNDANCY : 6.600
REMARK 200 R MERGE (I) : 0.08000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29
REMARK 200 COMPLETENESS FOR SHELL (%) : 81.2
REMARK 200 DATA REDUNDANCY IN SHELL : 4.20
REMARK 200 R MERGE FOR SHELL (I) : 0.19000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500
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 2YKZ
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 55.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70
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 120.57600
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 60.28800
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 90.43200
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 30.14400
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 150.72000
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 120.57600
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 60.28800
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 30.14400
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 90.43200
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 150.72000
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: 5510 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 12370 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -106.6 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 90.43200
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 A2042 LIES ON A SPECIAL POSITION.
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 1.70
REMARK 500 FE HEC A 128 C CMO A 129 1.79
REMARK 500 NE2 GLN A 84 O HOH A 2190 2.17
REMARK 500 O HOH A 2082 O HOH A 2176 2.19
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 LEU A 16 CB - CG - CD1 ANGL. DEV. = 11.0 DEGREES
REMARK 500 CYS A 116 CA - CB - SG ANGL. DEV. = 6.8 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 ASP A 75 56.71 -119.62
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 A2049 DISTANCE = 5.84 ANGSTROMS
REMARK 525 HOH A2123 DISTANCE = 6.69 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 92.6
REMARK 620 3 HEC A 128 NB 90.1 90.5
REMARK 620 4 HEC A 128 NC 89.4 177.8 90.3
REMARK 620 5 HEC A 128 ND 92.4 89.5 177.5 89.6
REMARK 620 6 CMO A 129 O 161.8 104.3 83.4 73.7 94.2
REMARK 620 N 1 2 3 4 5
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: 2YLI RELATED DB: PDB
REMARK 900 RECOMBINANT NATIVE CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS
REMARK 900 IN ITS FERROUS FORM AT 1.45 A
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: 1CGN RELATED DB: PDB
REMARK 900 CYTOCHROME C'
REMARK 900 RELATED ID: 2YLG RELATED DB: PDB
REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: ASCORBATE AND
REMARK 900 CARBON MONOOXIDE BOUND L16A VARIANT AT 1 .05 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: 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: 2XLW RELATED DB: PDB
REMARK 900 CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: FERROUS R124Q
REMARK 900 VARIANT WITH BOUND NO
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: 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
DBREF 2YLD A 1 127 UNP P00138 CYCP_ALCXX 1 127
SEQRES 1 A 127 PCA PHE ALA LYS PRO GLU ASP ALA VAL LYS TYR ARG GLN
SEQRES 2 A 127 SER ALA LEU 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 2YLD PCA A 1 GLU PYROGLUTAMIC ACID
HET PCA A 1 15
HET HEC A 128 77
HET CMO A 129 4
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 *253(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 PRO A 55 PHE A 59 5 5
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 1.82
LINK SG CYS A 119 CAC HEC A 128 1555 1555 1.91
LINK NE2 HIS A 120 FE HEC A 128 1555 1555 2.04
LINK FE HEC A 128 O ACMO A 129 1555 1555 2.80
CRYST1 53.914 53.914 180.864 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 0.018548 0.010709 0.000000 0.00000
SCALE2 0.000000 0.021417 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005529 0.00000
HETATM 1 N PCA A 1 -8.552 29.452 32.230 1.00 12.88 N
ANISOU 1 N PCA A 1 2299 2127 468 -220 -209 160 N
HETATM 2 CA PCA A 1 -9.319 29.719 33.416 1.00 12.81 C
ANISOU 2 CA PCA A 1 2286 2078 504 -251 -139 211 C
HETATM 3 CB PCA A 1 -8.620 28.834 34.446 1.00 13.85 C
ANISOU 3 CB PCA A 1 2688 2147 428 -245 -321 242 C
HETATM 4 CG PCA A 1 -7.183 28.736 33.961 1.00 14.34 C
ANISOU 4 CG PCA A 1 2509 2360 581 -222 -500 197 C
HETATM 5 CD PCA A 1 -7.306 28.970 32.487 1.00 12.98 C
ANISOU 5 CD PCA A 1 2250 2184 497 -103 -209 -46 C
HETATM 6 OE PCA A 1 -6.419 28.780 31.672 1.00 14.69 O
ANISOU 6 OE PCA A 1 2290 2545 747 31 -450 25 O
HETATM 7 C PCA A 1 -9.343 31.172 33.806 1.00 12.84 C
ANISOU 7 C PCA A 1 2333 1984 560 -212 -57 198 C
HETATM 8 O PCA A 1 -9.778 31.487 34.906 1.00 15.42 O
ANISOU 8 O PCA A 1 2838 2439 580 -47 66 -29 O
HETATM 9 H PCA A 1 -8.803 30.039 31.515 1.00 12.75 H
ANISOU 9 H PCA A 1 2256 2068 520 -225 -199 162 H
HETATM 10 HA PCA A 1 -10.239 29.396 33.305 1.00 12.95 H
ANISOU 10 HA PCA A 1 2337 2068 517 -239 -218 192 H
HETATM 11 HB2 PCA A 1 -9.086 27.974 34.509 1.00 13.18 H
ANISOU 11 HB2 PCA A 1 2382 2087 539 -210 -215 198 H
HETATM 12 HB3 PCA A 1 -8.640 29.253 35.331 1.00 13.18 H
ANISOU 12 HB3 PCA A 1 2380 2079 550 -236 -239 188 H
HETATM 13 HG2 PCA A 1 -6.798 27.881 34.244 1.00 14.05 H
ANISOU 13 HG2 PCA A 1 2507 2258 573 -241 -417 181 H
HETATM 14 HG3 PCA A 1 -6.656 29.454 34.365 1.00 13.87 H
ANISOU 14 HG3 PCA A 1 2463 2239 568 -195 -383 167 H
HETATM 15 HN2 PCA A 1 -9.161 28.715 32.236 1.00 12.78 H
ANISOU 15 HN2 PCA A 1 2257 2094 504 -201 -217 131 H
(ATOM LINES ARE NOT SHOWN.)
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