HEADER ELECTRON TRANSPORT 26-FEB-13 4JE9 TITLE CRYSTAL STRUCTURE OF AN ENGINEERED METAL-FREE RIDC1 CONSTRUCT WITH TITLE 2 FOUR INTERFACIAL DISULFIDE BONDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUBLE CYTOCHROME B562; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 23-128; COMPND 5 SYNONYM: CYTOCHROME B-562; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CYBC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS FOUR-HELIX BUNDLE, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR F.A.TEZCAN,A.M.MEDINA-MORALES,A.PEREZ,J.D.BRODIN REVDAT 3 20-SEP-23 4JE9 1 REMARK SEQADV LINK REVDAT 2 28-AUG-13 4JE9 1 JRNL REVDAT 1 21-AUG-13 4JE9 0 JRNL AUTH A.MEDINA-MORALES,A.PEREZ,J.D.BRODIN,F.A.TEZCAN JRNL TITL IN VITRO AND CELLULAR SELF-ASSEMBLY OF A ZN-BINDING PROTEIN JRNL TITL 2 CRYPTAND VIA TEMPLATED DISULFIDE BONDS. JRNL REF J.AM.CHEM.SOC. V. 135 12013 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 23905754 JRNL DOI 10.1021/JA405318D REMARK 2 REMARK 2 RESOLUTION. 2.12 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 13425 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) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.302 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.200 REMARK 3 FREE R VALUE TEST SET COUNT : 964 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) : 2.12 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 675 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.4140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1630 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : -1.32000 REMARK 3 B33 (A**2) : 0.87000 REMARK 3 B12 (A**2) : 0.00000 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): 0.285 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.249 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.217 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.957 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1768 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2423 ; 1.877 ; 2.091 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 214 ; 5.196 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 80 ;43.008 ;26.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 289 ;19.135 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;16.121 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 248 ; 0.122 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1364 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1068 ; 0.794 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1694 ; 1.369 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 700 ; 2.390 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 727 ; 3.336 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 0 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 422 ; 0.220 ; 0.050 REMARK 3 MEDIUM POSITIONAL 1 A (A): 378 ; 0.430 ; 0.500 REMARK 3 TIGHT THERMAL 1 A (A**2): 422 ; 1.050 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 378 ; 1.420 ; 2.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 201 REMARK 3 ORIGIN FOR THE GROUP (A): 12.4120 -21.6027 -14.1201 REMARK 3 T TENSOR REMARK 3 T11: 0.2126 T22: 0.1671 REMARK 3 T33: 0.2372 T12: -0.1106 REMARK 3 T13: 0.0515 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 3.1167 L22: 11.1750 REMARK 3 L33: 1.8335 L12: -0.4801 REMARK 3 L13: 0.1747 L23: 1.0574 REMARK 3 S TENSOR REMARK 3 S11: -0.0560 S12: 0.0591 S13: -0.2313 REMARK 3 S21: -0.1509 S22: -0.0451 S23: -0.5607 REMARK 3 S31: -0.0213 S32: 0.3184 S33: 0.1010 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 201 REMARK 3 ORIGIN FOR THE GROUP (A): -9.2026 -28.3126 -12.0928 REMARK 3 T TENSOR REMARK 3 T11: 0.2135 T22: 0.1457 REMARK 3 T33: 0.2450 T12: -0.0539 REMARK 3 T13: 0.1125 T23: 0.0427 REMARK 3 L TENSOR REMARK 3 L11: 6.1707 L22: 5.7287 REMARK 3 L33: 4.5493 L12: -0.6882 REMARK 3 L13: -1.5453 L23: 0.4466 REMARK 3 S TENSOR REMARK 3 S11: 0.3755 S12: 0.2131 S13: 0.7288 REMARK 3 S21: 0.1009 S22: -0.1727 S23: 0.1599 REMARK 3 S31: -0.2932 S32: -0.5954 S33: -0.2027 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 4JE9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000077935. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 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 : LIQUID NITROGEN-COOLED DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : K-B FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13444 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.120 REMARK 200 RESOLUTION RANGE LOW (A) : 48.023 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04000 REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.49900 REMARK 200 R SYM FOR SHELL (I) : 0.49900 REMARK 200 FOR SHELL : 1.500 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: 3IQ6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% METHYL-PENTANEDIOL, 0.1M TRIS PH REMARK 280 8.5, 0.2M SODIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 48.02300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.02300 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 28.08300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.89400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.08300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.89400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.02300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.08300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.89400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.02300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.08300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.89400 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 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 -48.02300 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 4 CG CD OE1 OE2 REMARK 480 GLU B 4 CG CD OE1 OE2 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 SG CYS B 98 CAB HEM B 201 1.89 REMARK 500 SG CYS A 98 CAB HEM A 201 2.03 REMARK 500 SG CYS A 101 CAC HEM A 201 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 4 CB GLU B 4 CG 0.300 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 76 CA - CB - CG ANGL. DEV. = 16.8 DEGREES REMARK 500 LEU B 10 CB - CG - CD1 ANGL. DEV. = 11.1 DEGREES REMARK 500 ASP B 74 CB - CG - OD2 ANGL. DEV. = 5.7 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 TRP A 41 -32.31 -30.81 REMARK 500 LYS A 83 78.96 -65.16 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 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 7 SD REMARK 620 2 HEM A 201 NA 91.2 REMARK 620 3 HEM A 201 NB 85.9 89.6 REMARK 620 4 HEM A 201 NC 89.6 179.1 90.0 REMARK 620 5 HEM A 201 ND 95.4 89.8 178.6 90.6 REMARK 620 6 HIS A 102 NE2 170.3 88.8 84.4 90.3 94.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B 7 SD REMARK 620 2 HEM B 201 NA 93.4 REMARK 620 3 HEM B 201 NB 84.8 87.3 REMARK 620 4 HEM B 201 NC 89.1 176.8 90.9 REMARK 620 5 HEM B 201 ND 94.8 94.8 177.8 87.0 REMARK 620 6 HIS B 102 NE2 166.6 89.7 82.3 87.5 97.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HNK RELATED DB: PDB REMARK 900 DIMERIC ASSEMBLY OF RIDC1 REMARK 900 RELATED ID: 2BC5 RELATED DB: PDB REMARK 900 CYTOCHROME B562 WITH ENGINEERED C-TYPE HEME LINKAGES REMARK 900 RELATED ID: 2QLA RELATED DB: PDB REMARK 900 ZINC-MEDIATED ASSEMBLY OF MBPC1 REMARK 900 RELATED ID: 3IQ5 RELATED DB: PDB REMARK 900 METAL-FREE TETRAMERIC CYTOCHROME CB562 COMPLEX WITH TWO INTERFACIAL REMARK 900 DISULFIDE BONDS REMARK 900 RELATED ID: 3IQ6 RELATED DB: PDB REMARK 900 ZN(II) MEDIATED TETRAMERIC CYTOCHROME CB562 COMPLEX WITH TWO REMARK 900 INTERFACIAL DISULFIDE BONDS REMARK 900 RELATED ID: 3HNI RELATED DB: PDB REMARK 900 ZN MEDIATED RIDC1 TETRAMER REMARK 900 RELATED ID: 4JEA RELATED DB: PDB REMARK 900 ENGINEERED ZN-RIDC1 CONSTRUCT WITH FOUR INTERFACIAL DISULFIDE BONDS REMARK 900 RELATED ID: 4JEB RELATED DB: PDB REMARK 900 ENGINEERED RIDC1 TETRAMER WITH FOUR INTERFACIAL DISULFIDE BONDS AND REMARK 900 FOUR THREE-COORDINATE ZN(II) SITES DBREF 4JE9 A 1 106 UNP P0ABE7 C562_ECOLX 23 128 DBREF 4JE9 B 1 106 UNP P0ABE7 C562_ECOLX 23 128 SEQADV 4JE9 ALA A 34 UNP P0ABE7 ARG 56 ENGINEERED MUTATION SEQADV 4JE9 ALA A 38 UNP P0ABE7 LEU 60 ENGINEERED MUTATION SEQADV 4JE9 TRP A 41 UNP P0ABE7 GLN 63 ENGINEERED MUTATION SEQADV 4JE9 SER A 42 UNP P0ABE7 LYS 64 ENGINEERED MUTATION SEQADV 4JE9 HIS A 59 UNP P0ABE7 LYS 81 ENGINEERED MUTATION SEQADV 4JE9 TRP A 66 UNP P0ABE7 ASP 88 ENGINEERED MUTATION SEQADV 4JE9 ILE A 69 UNP P0ABE7 VAL 91 ENGINEERED MUTATION SEQADV 4JE9 HIS A 73 UNP P0ABE7 ASP 95 ENGINEERED MUTATION SEQADV 4JE9 HIS A 77 UNP P0ABE7 LYS 99 ENGINEERED MUTATION SEQADV 4JE9 CYS A 81 UNP P0ABE7 GLU 103 ENGINEERED MUTATION SEQADV 4JE9 CYS A 96 UNP P0ABE7 THR 118 ENGINEERED MUTATION SEQADV 4JE9 CYS A 98 UNP P0ABE7 ARG 120 ENGINEERED MUTATION SEQADV 4JE9 CYS A 101 UNP P0ABE7 TYR 123 ENGINEERED MUTATION SEQADV 4JE9 ALA B 34 UNP P0ABE7 ARG 56 ENGINEERED MUTATION SEQADV 4JE9 ALA B 38 UNP P0ABE7 LEU 60 ENGINEERED MUTATION SEQADV 4JE9 TRP B 41 UNP P0ABE7 GLN 63 ENGINEERED MUTATION SEQADV 4JE9 SER B 42 UNP P0ABE7 LYS 64 ENGINEERED MUTATION SEQADV 4JE9 HIS B 59 UNP P0ABE7 LYS 81 ENGINEERED MUTATION SEQADV 4JE9 TRP B 66 UNP P0ABE7 ASP 88 ENGINEERED MUTATION SEQADV 4JE9 ILE B 69 UNP P0ABE7 VAL 91 ENGINEERED MUTATION SEQADV 4JE9 HIS B 73 UNP P0ABE7 ASP 95 ENGINEERED MUTATION SEQADV 4JE9 HIS B 77 UNP P0ABE7 LYS 99 ENGINEERED MUTATION SEQADV 4JE9 CYS B 81 UNP P0ABE7 GLU 103 ENGINEERED MUTATION SEQADV 4JE9 CYS B 96 UNP P0ABE7 THR 118 ENGINEERED MUTATION SEQADV 4JE9 CYS B 98 UNP P0ABE7 ARG 120 ENGINEERED MUTATION SEQADV 4JE9 CYS B 101 UNP P0ABE7 TYR 123 ENGINEERED MUTATION SEQRES 1 A 106 ALA ASP LEU GLU ASP ASN MET GLU THR LEU ASN ASP ASN SEQRES 2 A 106 LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA ALA GLN VAL SEQRES 3 A 106 LYS ASP ALA LEU THR LYS MET ALA ALA ALA ALA ALA ASP SEQRES 4 A 106 ALA TRP SER ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 A 106 PRO ASP SER PRO GLU MET HIS ASP PHE ARG HIS GLY PHE SEQRES 6 A 106 TRP ILE LEU ILE GLY GLN ILE HIS ASP ALA LEU HIS LEU SEQRES 7 A 106 ALA ASN CYS GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 A 106 GLU GLN LEU LYS CYS THR CYS ASN ALA CYS HIS GLN LYS SEQRES 9 A 106 TYR ARG SEQRES 1 B 106 ALA ASP LEU GLU ASP ASN MET GLU THR LEU ASN ASP ASN SEQRES 2 B 106 LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA ALA GLN VAL SEQRES 3 B 106 LYS ASP ALA LEU THR LYS MET ALA ALA ALA ALA ALA ASP SEQRES 4 B 106 ALA TRP SER ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 B 106 PRO ASP SER PRO GLU MET HIS ASP PHE ARG HIS GLY PHE SEQRES 6 B 106 TRP ILE LEU ILE GLY GLN ILE HIS ASP ALA LEU HIS LEU SEQRES 7 B 106 ALA ASN CYS GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 B 106 GLU GLN LEU LYS CYS THR CYS ASN ALA CYS HIS GLN LYS SEQRES 9 B 106 TYR ARG HET HEM A 201 43 HET HEM B 201 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 HOH *36(H2 O) HELIX 1 1 ASP A 2 ALA A 20 1 19 HELIX 2 2 ASN A 22 TRP A 41 1 20 HELIX 3 3 PRO A 45 GLU A 49 5 5 HELIX 4 4 SER A 55 CYS A 81 1 27 HELIX 5 5 LYS A 83 ARG A 106 1 24 HELIX 6 6 ASP B 2 ALA B 20 1 19 HELIX 7 7 ASN B 22 TRP B 41 1 20 HELIX 8 8 PRO B 45 GLU B 49 5 5 HELIX 9 9 SER B 55 CYS B 81 1 27 HELIX 10 10 LYS B 83 ARG B 106 1 24 SSBOND 1 CYS A 81 CYS A 81 1555 3554 2.07 SSBOND 2 CYS A 96 CYS B 96 1555 1555 2.07 SSBOND 3 CYS B 81 CYS B 81 1555 3554 2.10 LINK SD MET A 7 FE HEM A 201 1555 1555 2.41 LINK NE2 HIS A 102 FE HEM A 201 1555 1555 2.03 LINK SD MET B 7 FE HEM B 201 1555 1555 2.28 LINK NE2 HIS B 102 FE HEM B 201 1555 1555 1.93 SITE 1 AC1 12 MET A 7 ASN A 11 PRO A 45 PRO A 46 SITE 2 AC1 12 PHE A 61 PHE A 65 CYS A 98 CYS A 101 SITE 3 AC1 12 HIS A 102 TYR A 105 ARG A 106 ARG B 106 SITE 1 AC2 9 MET B 7 LEU B 14 PRO B 45 PHE B 61 SITE 2 AC2 9 PHE B 65 CYS B 98 CYS B 101 HIS B 102 SITE 3 AC2 9 ARG B 106 CRYST1 56.166 87.788 96.046 90.00 90.00 90.00 C 2 2 21 16 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 0.017804 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011391 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010412 0.00000