PDB Short entry for 3BVD HEADER OXIDOREDUCTASE 07-JAN-08 3BVD TITLE STRUCTURE OF SURFACE-ENGINEERED CYTOCHROME BA3 OXIDASE FROM THERMUS TITLE 2 THERMOPHILUS UNDER XENON PRESSURE, 100PSI 5MIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C OXIDASE SUBUNIT 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE I, CYTOCHROME C BA3, COMPND 5 SUBUNIT I, CYTOCHROME CBA3 SUBUNIT 1; COMPND 6 EC: 1.9.3.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: CYTOCHROME C OXIDASE SUBUNIT 2; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE II, CYTOCHROME C BA3, COMPND 13 SUBUNIT II, CYTOCHROME CBA3 SUBUNIT 2; COMPND 14 EC: 1.9.3.1; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES; COMPND 17 MOL_ID: 3; COMPND 18 MOLECULE: CYTOCHROME C OXIDASE POLYPEPTIDE 2A; COMPND 19 CHAIN: C; COMPND 20 SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE IIA, CYTOCHROME C BA3, COMPND 21 SUBUNIT IIA, CYTOCHROME CBA3 SUBUNIT 2A; COMPND 22 EC: 1.9.3.1; COMPND 23 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 STRAIN: HB8; SOURCE 4 ATCC: 27634; SOURCE 5 GENE: CBAA; SOURCE 6 EXPRESSION_SYSTEM: THERMUS THERMOPHILUS; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HB8; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMK18; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 12 STRAIN: HB8; SOURCE 13 ATCC: 27634; SOURCE 14 GENE: CBAB, CTAC; SOURCE 15 EXPRESSION_SYSTEM: THERMUS THERMOPHILUS; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: HB8; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PMK18; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 21 STRAIN: HB8; SOURCE 22 ATCC: 27634; SOURCE 23 GENE: CBAD; SOURCE 24 EXPRESSION_SYSTEM: THERMUS THERMOPHILUS; SOURCE 25 EXPRESSION_SYSTEM_STRAIN: HB8; SOURCE 26 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 27 EXPRESSION_SYSTEM_PLASMID: PMK18 KEYWDS CYTOCHROME BA3 OXIDASE, HEME, INTEGRAL MEMBRANE PROTEIN, COPPER, KEYWDS 2 ELECTRON TRANSPORT, HYDROGEN ION TRANSPORT, ION TRANSPORT, IRON, KEYWDS 3 METAL-BINDING, OXIDOREDUCTASE, RESPIRATORY CHAIN, TRANSMEMBRANE, KEYWDS 4 TRANSPORT, FORMYLATION, XENON EXPDTA X-RAY DIFFRACTION AUTHOR V.M.LUNA,Y.CHEN,J.A.FEE,C.D.STOUT REVDAT 5 30-AUG-23 3BVD 1 REMARK REVDAT 4 20-OCT-21 3BVD 1 REMARK SEQADV REVDAT 3 25-OCT-17 3BVD 1 REMARK REVDAT 2 24-FEB-09 3BVD 1 VERSN REVDAT 1 20-MAY-08 3BVD 0 JRNL AUTH V.M.LUNA,Y.CHEN,J.A.FEE,C.D.STOUT JRNL TITL CRYSTALLOGRAPHIC STUDIES OF XE AND KR BINDING WITHIN THE JRNL TITL 2 LARGE INTERNAL CAVITY OF CYTOCHROME BA3 FROM THERMUS JRNL TITL 3 THERMOPHILUS: STRUCTURAL ANALYSIS AND ROLE OF OXYGEN JRNL TITL 4 TRANSPORT CHANNELS IN THE HEME-CU OXIDASES. JRNL REF BIOCHEMISTRY V. 47 4657 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18376849 JRNL DOI 10.1021/BI800045Y REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.LIU,V.M.LUNA,Y.CHEN,C.D.STOUT,J.A.FEE REMARK 1 TITL AN UNEXPECTED OUTCOME OF SURFACE ENGINEERING AN INTEGRAL REMARK 1 TITL 2 MEMBRANE PROTEIN: IMPROVED CRYSTALLIZATION OF CYTOCHROME BA3 REMARK 1 TITL 3 FROM THERMUS THERMOPHILUS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 63 1029 2007 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 18084085 REMARK 1 DOI 10.1107/S1744309107054176 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.M.HUNSICKER-WANG,R.L.PACOMA,Y.CHEN,J.A.FEE,C.D.STOUT REMARK 1 TITL A NOVEL CRYOPROTECTION SCHEME FOR ENCHANCING THE DIFFRACTION REMARK 1 TITL 2 OF CRYSTALS OF RECOMBINANT CYTOCHROME BA3 OXIDASE FROM REMARK 1 TITL 3 THERMUS THERMOPHILUS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 61 340 2005 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 15735345 REMARK 1 DOI 10.1107/S0907444904033906 REMARK 2 REMARK 2 RESOLUTION. 3.37 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) : 3.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16329 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.292 REMARK 3 FREE R VALUE : 0.336 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 823 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) : 3.37 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2513 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3490 REMARK 3 BIN FREE R VALUE SET COUNT : 147 REMARK 3 BIN FREE R VALUE : 0.4420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5907 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 118 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 108.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 85.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.07000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.712 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.624 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 38.250 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.891 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.826 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6230 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8563 ; 1.304 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 746 ; 5.323 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 232 ;36.125 ;22.241 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 898 ;19.271 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.676 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 952 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4734 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3418 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4246 ; 0.311 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 170 ; 0.127 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.211 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 38 ; 0.277 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.099 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 3BVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000046002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SIDE-SCATTERING CUBEROOT I-BEAM REMARK 200 BENT SINGLE CRYSTAL; ASYMMETRIC REMARK 200 CUT 12.2 DEGS. REMARK 200 OPTICS : VERTICAL FOCUSING MIRROR; SINGLE REMARK 200 CRYSTAL SI(311) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16341 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.370 REMARK 200 RESOLUTION RANGE LOW (A) : 27.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.46300 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, REFMAC 5.2.0019, CNS REMARK 200 STARTING MODEL: PDB ENTRY 1XME REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6-9% PEG 2000, 50MM KCL, 7.5-30MM BIS REMARK 280 -TRIS PH 7.0, 6.5MM NONYL-B-D-GLUCOPYRANOSIDE , VAPOR DIFFUSION, REMARK 280 TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 76.76750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 59.86300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 59.86300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 38.38375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 59.86300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 59.86300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 115.15125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 59.86300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 59.86300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 38.38375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 59.86300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.86300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 115.15125 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 76.76750 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -149.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 MET A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 ALA A 2 REMARK 465 VAL A 3 REMARK 465 ARG A 4 REMARK 465 ALA A 5 REMARK 465 SER A 6 REMARK 465 GLU A 7 REMARK 465 ILE A 8 REMARK 465 SER A 9 REMARK 465 ARG A 10 REMARK 465 VAL A 11 REMARK 465 TYR A 12 REMARK 465 MET B 1 REMARK 465 VAL B 2 REMARK 465 MET C 1 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 98 -21.01 75.77 REMARK 500 ASN A 102 95.43 -56.57 REMARK 500 THR A 130 74.64 -63.12 REMARK 500 LEU A 132 160.57 70.38 REMARK 500 PHE A 135 59.19 37.36 REMARK 500 PRO A 278 47.14 -83.09 REMARK 500 PRO A 292 -37.15 -39.12 REMARK 500 ARG A 330 -89.47 -105.36 REMARK 500 TRP A 341 3.83 -68.43 REMARK 500 SER A 368 42.23 -87.15 REMARK 500 PHE A 369 -94.41 48.38 REMARK 500 GLN A 388 -64.79 -105.30 REMARK 500 SER A 391 -73.81 -103.45 REMARK 500 SER A 400 23.99 -71.46 REMARK 500 SER A 414 -150.76 -80.64 REMARK 500 ASN A 446 13.79 81.54 REMARK 500 VAL A 456 78.36 -118.92 REMARK 500 LEU A 483 -35.94 -35.77 REMARK 500 PHE A 489 38.22 -78.40 REMARK 500 GLU A 496 47.26 -77.78 REMARK 500 PRO A 499 24.36 -68.24 REMARK 500 PRO A 505 156.08 -49.98 REMARK 500 HIS A 552 21.64 -143.25 REMARK 500 GLN B 4 -89.67 58.20 REMARK 500 HIS B 8 -29.00 -147.67 REMARK 500 THR B 41 -8.88 -57.52 REMARK 500 THR B 57 46.66 -108.66 REMARK 500 PRO B 63 -9.53 -58.09 REMARK 500 ALA B 65 -60.82 -90.36 REMARK 500 THR B 74 32.53 -141.52 REMARK 500 PHE B 86 -167.35 -120.97 REMARK 500 ALA B 87 83.60 -58.61 REMARK 500 PHE B 88 41.40 70.13 REMARK 500 ASP B 111 -82.06 -149.42 REMARK 500 LYS B 167 179.21 -57.82 REMARK 500 LYS C 4 103.68 68.10 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 800 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 72 NE2 REMARK 620 2 HEM A 800 NA 92.0 REMARK 620 3 HEM A 800 NB 92.2 88.8 REMARK 620 4 HEM A 800 NC 85.3 176.2 88.6 REMARK 620 5 HEM A 800 ND 86.8 92.7 178.2 89.8 REMARK 620 6 HIS A 386 NE2 178.3 89.7 88.2 93.1 92.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 803 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 282 NE2 REMARK 620 2 HIS A 283 NE2 94.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CUA B 802 CU2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 114 ND1 REMARK 620 2 CUA B 802 CU1 131.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CUA B 802 CU1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN B 151 O REMARK 620 2 CUA B 802 CU2 117.8 REMARK 620 3 HIS B 157 ND1 84.6 157.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HAS A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CUA B 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 807 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 808 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 809 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 810 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QPD RELATED DB: PDB REMARK 900 SURFACE-ENGINEERED CYTOCHROME BA3 OXIDASE DBREF 3BVD A 2 562 UNP Q5SJ79 COX1_THET8 2 562 DBREF 3BVD B 1 168 UNP Q5SJ80 COX2_THET8 1 168 DBREF 3BVD C 1 34 UNP P82543 COXA_THET8 1 34 SEQADV 3BVD MET A -5 UNP Q5SJ79 EXPRESSION TAG SEQADV 3BVD HIS A -4 UNP Q5SJ79 EXPRESSION TAG SEQADV 3BVD HIS A -3 UNP Q5SJ79 EXPRESSION TAG SEQADV 3BVD HIS A -2 UNP Q5SJ79 EXPRESSION TAG SEQADV 3BVD HIS A -1 UNP Q5SJ79 EXPRESSION TAG SEQADV 3BVD HIS A 0 UNP Q5SJ79 EXPRESSION TAG SEQADV 3BVD HIS A 1 UNP Q5SJ79 EXPRESSION TAG SEQADV 3BVD ARG A 258 UNP Q5SJ79 LYS 258 ENGINEERED MUTATION SEQADV 3BVD GLN B 4 UNP Q5SJ80 GLU 4 ENGINEERED MUTATION SEQRES 1 A 568 MET HIS HIS HIS HIS HIS HIS ALA VAL ARG ALA SER GLU SEQRES 2 A 568 ILE SER ARG VAL TYR GLU ALA TYR PRO GLU LYS LYS ALA SEQRES 3 A 568 THR LEU TYR PHE LEU VAL LEU GLY PHE LEU ALA LEU ILE SEQRES 4 A 568 VAL GLY SER LEU PHE GLY PRO PHE GLN ALA LEU ASN TYR SEQRES 5 A 568 GLY ASN VAL ASP ALA TYR PRO LEU LEU LYS ARG LEU LEU SEQRES 6 A 568 PRO PHE VAL GLN SER TYR TYR GLN GLY LEU THR LEU HIS SEQRES 7 A 568 GLY VAL LEU ASN ALA ILE VAL PHE THR GLN LEU PHE ALA SEQRES 8 A 568 GLN ALA ILE MET VAL TYR LEU PRO ALA ARG GLU LEU ASN SEQRES 9 A 568 MET ARG PRO ASN MET GLY LEU MET TRP LEU SER TRP TRP SEQRES 10 A 568 MET ALA PHE ILE GLY LEU VAL VAL ALA ALA LEU PRO LEU SEQRES 11 A 568 LEU ALA ASN GLU ALA THR VAL LEU TYR THR PHE TYR PRO SEQRES 12 A 568 PRO LEU LYS GLY HIS TRP ALA PHE TYR LEU GLY ALA SER SEQRES 13 A 568 VAL PHE VAL LEU SER THR TRP VAL SER ILE TYR ILE VAL SEQRES 14 A 568 LEU ASP LEU TRP ARG ARG TRP LYS ALA ALA ASN PRO GLY SEQRES 15 A 568 LYS VAL THR PRO LEU VAL THR TYR MET ALA VAL VAL PHE SEQRES 16 A 568 TRP LEU MET TRP PHE LEU ALA SER LEU GLY LEU VAL LEU SEQRES 17 A 568 GLU ALA VAL LEU PHE LEU LEU PRO TRP SER PHE GLY LEU SEQRES 18 A 568 VAL GLU GLY VAL ASP PRO LEU VAL ALA ARG THR LEU PHE SEQRES 19 A 568 TRP TRP THR GLY HIS PRO ILE VAL TYR PHE TRP LEU LEU SEQRES 20 A 568 PRO ALA TYR ALA ILE ILE TYR THR ILE LEU PRO LYS GLN SEQRES 21 A 568 ALA GLY GLY ARG LEU VAL SER ASP PRO MET ALA ARG LEU SEQRES 22 A 568 ALA PHE LEU LEU PHE LEU LEU LEU SER THR PRO VAL GLY SEQRES 23 A 568 PHE HIS HIS GLN PHE ALA ASP PRO GLY ILE ASP PRO THR SEQRES 24 A 568 TRP LYS MET ILE HIS SER VAL LEU THR LEU PHE VAL ALA SEQRES 25 A 568 VAL PRO SER LEU MET THR ALA PHE THR VAL ALA ALA SER SEQRES 26 A 568 LEU GLU PHE ALA GLY ARG LEU ARG GLY GLY ARG GLY LEU SEQRES 27 A 568 PHE GLY TRP ILE ARG ALA LEU PRO TRP ASP ASN PRO ALA SEQRES 28 A 568 PHE VAL ALA PRO VAL LEU GLY LEU LEU GLY PHE ILE PRO SEQRES 29 A 568 GLY GLY ALA GLY GLY ILE VAL ASN ALA SER PHE THR LEU SEQRES 30 A 568 ASP TYR VAL VAL HIS ASN THR ALA TRP VAL PRO GLY HIS SEQRES 31 A 568 PHE HIS LEU GLN VAL ALA SER LEU VAL THR LEU THR ALA SEQRES 32 A 568 MET GLY SER LEU TYR TRP LEU LEU PRO ASN LEU THR GLY SEQRES 33 A 568 LYS PRO ILE SER ASP ALA GLN ARG ARG LEU GLY LEU ALA SEQRES 34 A 568 VAL VAL TRP LEU TRP PHE LEU GLY MET MET ILE MET ALA SEQRES 35 A 568 VAL GLY LEU HIS TRP ALA GLY LEU LEU ASN VAL PRO ARG SEQRES 36 A 568 ARG ALA TYR ILE ALA GLN VAL PRO ASP ALA TYR PRO HIS SEQRES 37 A 568 ALA ALA VAL PRO MET VAL PHE ASN VAL LEU ALA GLY ILE SEQRES 38 A 568 VAL LEU LEU VAL ALA LEU LEU LEU PHE ILE TYR GLY LEU SEQRES 39 A 568 PHE SER VAL LEU LEU SER ARG GLU ARG LYS PRO GLU LEU SEQRES 40 A 568 ALA GLU ALA PRO LEU PRO PHE ALA GLU VAL ILE SER GLY SEQRES 41 A 568 PRO GLU ASP ARG ARG LEU VAL LEU ALA MET ASP ARG ILE SEQRES 42 A 568 GLY PHE TRP PHE ALA VAL ALA ALA ILE LEU VAL VAL LEU SEQRES 43 A 568 ALA TYR GLY PRO THR LEU VAL GLN LEU PHE GLY HIS LEU SEQRES 44 A 568 ASN PRO VAL PRO GLY TRP ARG LEU TRP SEQRES 1 B 168 MET VAL ASP GLN HIS LYS ALA HIS LYS ALA ILE LEU ALA SEQRES 2 B 168 TYR GLU LYS GLY TRP LEU ALA PHE SER LEU ALA MET LEU SEQRES 3 B 168 PHE VAL PHE ILE ALA LEU ILE ALA TYR THR LEU ALA THR SEQRES 4 B 168 HIS THR ALA GLY VAL ILE PRO ALA GLY LYS LEU GLU ARG SEQRES 5 B 168 VAL ASP PRO THR THR VAL ARG GLN GLU GLY PRO TRP ALA SEQRES 6 B 168 ASP PRO ALA GLN ALA VAL VAL GLN THR GLY PRO ASN GLN SEQRES 7 B 168 TYR THR VAL TYR VAL LEU ALA PHE ALA PHE GLY TYR GLN SEQRES 8 B 168 PRO ASN PRO ILE GLU VAL PRO GLN GLY ALA GLU ILE VAL SEQRES 9 B 168 PHE LYS ILE THR SER PRO ASP VAL ILE HIS GLY PHE HIS SEQRES 10 B 168 VAL GLU GLY THR ASN ILE ASN VAL GLU VAL LEU PRO GLY SEQRES 11 B 168 GLU VAL SER THR VAL ARG TYR THR PHE LYS ARG PRO GLY SEQRES 12 B 168 GLU TYR ARG ILE ILE CYS ASN GLN TYR CYS GLY LEU GLY SEQRES 13 B 168 HIS GLN ASN MET PHE GLY THR ILE VAL VAL LYS GLU SEQRES 1 C 34 MET GLU GLU LYS PRO LYS GLY ALA LEU ALA VAL ILE LEU SEQRES 2 C 34 VAL LEU THR LEU THR ILE LEU VAL PHE TRP LEU GLY VAL SEQRES 3 C 34 TYR ALA VAL PHE PHE ALA ARG GLY HET CU A 803 1 HET HEM A 800 43 HET HAS A 801 65 HET XE A 805 1 HET XE A 806 1 HET XE A 807 1 HET XE A 808 1 HET XE A 809 1 HET XE A 810 1 HET XE A 811 1 HET CUA B 802 2 HETNAM CU COPPER (II) ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM HAS HEME-AS HETNAM XE XENON HETNAM CUA DINUCLEAR COPPER ION HETSYN HEM HEME FORMUL 4 CU CU 2+ FORMUL 5 HEM C34 H32 FE N4 O4 FORMUL 6 HAS C54 H64 FE N4 O6 FORMUL 7 XE 7(XE) FORMUL 14 CUA CU2 HELIX 1 1 PRO A 16 LEU A 37 1 22 HELIX 2 2 PHE A 38 TYR A 46 1 9 HELIX 3 3 ALA A 51 LEU A 59 1 9 HELIX 4 4 SER A 64 ILE A 78 1 15 HELIX 5 5 ILE A 78 ASN A 98 1 21 HELIX 6 6 ASN A 102 ALA A 126 1 25 HELIX 7 7 HIS A 142 ASN A 174 1 33 HELIX 8 8 PRO A 180 PHE A 207 1 28 HELIX 9 9 PHE A 207 GLY A 214 1 8 HELIX 10 10 ASP A 220 HIS A 233 1 14 HELIX 11 11 HIS A 233 ILE A 250 1 18 HELIX 12 12 ILE A 250 ALA A 255 1 6 HELIX 13 13 ASP A 262 SER A 276 1 15 HELIX 14 14 VAL A 279 GLN A 284 5 6 HELIX 15 15 ASP A 291 VAL A 305 1 15 HELIX 16 16 ALA A 306 ARG A 327 1 22 HELIX 17 17 ASN A 343 ALA A 367 1 25 HELIX 18 18 SER A 368 VAL A 375 5 8 HELIX 19 19 ALA A 379 HIS A 386 1 8 HELIX 20 20 SER A 391 SER A 400 1 10 HELIX 21 21 LEU A 404 GLY A 410 1 7 HELIX 22 22 ASP A 415 LEU A 445 1 31 HELIX 23 23 TYR A 452 HIS A 462 5 11 HELIX 24 24 ALA A 463 LEU A 492 1 30 HELIX 25 25 PRO A 499 ALA A 504 1 6 HELIX 26 26 ARG A 518 ASP A 525 1 8 HELIX 27 27 ARG A 526 GLY A 551 1 26 HELIX 28 28 ASP B 3 ALA B 7 5 5 HELIX 29 29 HIS B 8 THR B 39 1 32 HELIX 30 30 HIS B 40 ILE B 45 5 6 HELIX 31 31 ASP B 66 GLN B 69 5 4 HELIX 32 32 GLY B 156 ASN B 159 5 4 HELIX 33 33 PRO C 5 GLY C 34 1 30 SHEET 1 A 2 GLY A 218 VAL A 219 0 SHEET 2 A 2 VAL A 556 PRO A 557 -1 O VAL A 556 N VAL A 219 SHEET 1 B 3 VAL B 71 GLN B 73 0 SHEET 2 B 3 GLN B 78 PHE B 86 -1 O THR B 80 N VAL B 72 SHEET 3 B 3 GLY B 89 GLN B 91 -1 O GLN B 91 N LEU B 84 SHEET 1 C 4 VAL B 71 GLN B 73 0 SHEET 2 C 4 GLN B 78 PHE B 86 -1 O THR B 80 N VAL B 72 SHEET 3 C 4 GLU B 102 THR B 108 1 O THR B 108 N ALA B 85 SHEET 4 C 4 SER B 133 THR B 138 -1 O VAL B 135 N PHE B 105 SHEET 1 D 5 ILE B 95 VAL B 97 0 SHEET 2 D 5 PHE B 161 VAL B 166 1 O VAL B 165 N ILE B 95 SHEET 3 D 5 GLY B 143 ILE B 148 -1 N ILE B 147 O GLY B 162 SHEET 4 D 5 HIS B 114 VAL B 118 -1 N HIS B 117 O ILE B 148 SHEET 5 D 5 ASN B 124 VAL B 127 -1 O VAL B 127 N HIS B 114 LINK NE2 HIS A 72 FE HEM A 800 1555 1555 2.20 LINK NE2 HIS A 282 CU CU A 803 1555 1555 2.03 LINK NE2 HIS A 283 CU CU A 803 1555 1555 2.19 LINK NE2 HIS A 386 FE HEM A 800 1555 1555 2.11 LINK ND1 HIS B 114 CU2 CUA B 802 1555 1555 2.29 LINK O GLN B 151 CU1 CUA B 802 1555 1555 2.17 LINK ND1 HIS B 157 CU1 CUA B 802 1555 1555 2.04 CISPEP 1 PRO A 137 PRO A 138 0 9.29 CISPEP 2 GLN B 91 PRO B 92 0 -3.38 CISPEP 3 ASN B 93 PRO B 94 0 9.40 SITE 1 AC1 3 HIS A 233 HIS A 282 HIS A 283 SITE 1 AC2 20 GLY A 39 PRO A 40 GLN A 42 ALA A 43 SITE 2 AC2 20 TYR A 46 TYR A 65 LEU A 69 HIS A 72 SITE 3 AC2 20 ASN A 76 ALA A 77 TYR A 133 PHE A 385 SITE 4 AC2 20 HIS A 386 VAL A 389 ALA A 390 THR A 394 SITE 5 AC2 20 MET A 432 ARG A 449 ARG A 450 ALA A 451 SITE 1 AC3 24 TYR A 133 TRP A 229 VAL A 236 TYR A 237 SITE 2 AC3 24 TRP A 239 HIS A 282 THR A 302 SER A 309 SITE 3 AC3 24 ALA A 313 ALA A 317 LEU A 353 LEU A 354 SITE 4 AC3 24 PHE A 356 GLY A 360 GLY A 363 ASN A 366 SITE 5 AC3 24 ALA A 367 ASP A 372 HIS A 376 VAL A 381 SITE 6 AC3 24 HIS A 384 PHE A 385 GLN A 388 ARG A 449 SITE 1 AC4 6 HIS B 114 CYS B 149 GLN B 151 CYS B 153 SITE 2 AC4 6 HIS B 157 MET B 160 SITE 1 AC5 2 TYR A 133 GLY A 232 SITE 1 AC6 1 LEU A 208 SITE 1 AC7 1 VAL A 201 SITE 1 AC8 2 PHE A 228 XE A 810 SITE 1 AC9 3 PHE A 228 GLY A 232 XE A 809 CRYST1 119.726 119.726 153.535 90.00 90.00 90.00 P 41 21 2 8 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 0.008352 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008352 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006513 0.00000