10 20 30 40 50 60 70 80 1BQK - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSPORT 17-AUG-98 1BQK
TITLE OXIDIZED PSEUDOAZURIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSEUDOAZURIN; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: OXIDIZED FORM OF PSEUDOAZURIN
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACHROMOBACTER CYCLOCLASTES; SOURCE 3 ORGANISM_TAXID: 223; SOURCE 4 STRAIN: IAM1013
KEYWDS CUPROPROTEIN, ELECTRON TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR T.INOUE,N.NISHIO,S.HAMANAKA,T.SHIMOMURA,S.HARADA,S.SUZUKI, AUTHOR 2 T.KOHZUMA,S.SHIDARA,H.IWASAKI,Y.KAI
REVDAT 2 24-FEB-09 1BQK 1 VERSN REVDAT 1 17-AUG-99 1BQK 0
JRNL AUTH T.INOUE,N.NISHIO,S.SUZUKI,K.KATAOKA,T.KOHZUMA,Y.KAI JRNL TITL CRYSTAL STRUCTURE DETERMINATIONS OF OXIDIZED AND JRNL TITL 2 REDUCED PSEUDOAZURINS FROM ACHROMOBACTER JRNL TITL 3 CYCLOCLASTES. CONCERTED MOVEMENT OF COPPER SITE IN JRNL TITL 4 REDOX FORMS WITH THE REARRANGEMENT OF HYDROGEN JRNL TITL 5 BOND AT A REMOTE HISTIDINE. JRNL REF J.BIOL.CHEM. V. 274 17845 1999 JRNL REFN ISSN 0021-9258 JRNL PMID 10364229 JRNL DOI 10.1074/JBC.274.25.17845
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 TITL CRYSTAL STRUCTURE DETERMINATIONS OF OXIDIZED AND REMARK 1 TITL 2 REDUCED PSEUDOAZURIN FROM ACHROMOBACTER REMARK 1 TITL 3 CYCLOCLASTES: A REDOX-INDUCED CONFORMATIONAL REMARK 1 TITL 4 CHANGE CONTAINS A PEPTIDE BOND FLIP REMARK 1 REF THESIS REMARK 1 PUBL UNIVERSITY (THESIS) REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH T.INOUE,N.NISHIO,Y.KAI,S.HARADA,Y.OHSHIRO,S.SUZUKI, REMARK 1 AUTH 2 T.KOHZUMA,S.SHIDARA,H.IWASAKI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES ON REMARK 1 TITL 2 PSEUDOAZURIN FROM ACHROMOBACTER CYCLOCLASTES REMARK 1 TITL 3 IAM1013 REMARK 1 REF J.BIOCHEM.(TOKYO) V. 114 761 1993 REMARK 1 REFN ISSN 0021-924X
REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 3 NUMBER OF REFLECTIONS : 21303 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.178 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 : 1084 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 913 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.008 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.022 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.026 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.022 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.109 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.168 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.237 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.132 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 11.200; 15.000 REMARK 3 PLANAR (DEGREES) : 4.000 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 12.900; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 22.800; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.137 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.700 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.912 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.937 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ESTIMATED COORDINATE ERROR. ESD FROM REMARK 3 LUZZATI PLOT (A) : 0.137
REMARK 4 REMARK 4 1BQK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-93 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21303 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 200 DATA REDUNDANCY : 10.500 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.18200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1PZA REMARK 200 REMARK 200 REMARK: DATA WERE COLLECTED USING THE WEISSENBERG METHOD
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 28.36550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.04150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.77200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 15.04150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.36550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.77200 REMARK 290 SMTRY3 4 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: MONOMERIC 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 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 MET A 16 77.59 57.49 REMARK 500 ASN A 61 -2.79 77.45 REMARK 500 THR A 69 -72.61 -102.40 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 A 283 DISTANCE = 6.46 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 CU A 125 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 40 ND1 REMARK 620 2 CYS A 78 SG 135.3 REMARK 620 3 HIS A 81 ND1 100.3 114.5 REMARK 620 4 MET A 86 SD 86.8 107.4 107.4 REMARK 620 N 1 2 3
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: COP REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: OXIDIZED COPPER COORDINATION REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 125
DBREF 1BQK A 1 124 UNP P19567 AZUP_ACHCY 29 152
SEQRES 1 A 124 ALA ASP PHE GLU VAL HIS MET LEU ASN LYS GLY LYS ASP SEQRES 2 A 124 GLY ALA MET VAL PHE GLU PRO ALA SER LEU LYS VAL ALA SEQRES 3 A 124 PRO GLY ASP THR VAL THR PHE ILE PRO THR ASP LYS GLY SEQRES 4 A 124 HIS ASN VAL GLU THR ILE LYS GLY MET ILE PRO ASP GLY SEQRES 5 A 124 ALA GLU ALA PHE LYS SER LYS ILE ASN GLU ASN TYR LYS SEQRES 6 A 124 VAL THR PHE THR ALA PRO GLY VAL TYR GLY VAL LYS CYS SEQRES 7 A 124 THR PRO HIS TYR GLY MET GLY MET VAL GLY VAL VAL GLN SEQRES 8 A 124 VAL GLY ASP ALA PRO ALA ASN LEU GLU ALA VAL LYS GLY SEQRES 9 A 124 ALA LYS ASN PRO LYS LYS ALA GLN GLU ARG LEU ASP ALA SEQRES 10 A 124 ALA LEU ALA ALA LEU GLY ASN
HET CU A 125 1
HETNAM CU COPPER (II) ION
FORMUL 2 CU CU 2+ FORMUL 3 HOH *121(H2 O)
HELIX 1 1 THR A 79 MET A 84 5 6 HELIX 2 2 LEU A 99 GLY A 104 1 6 HELIX 3 3 LYS A 109 LEU A 122 1 14
SHEET 1 A 4 VAL A 17 GLU A 19 0 SHEET 2 A 4 ASP A 2 LEU A 8 -1 N LEU A 8 O VAL A 17 SHEET 3 A 4 THR A 30 ILE A 34 1 N THR A 30 O PHE A 3 SHEET 4 A 4 TYR A 64 THR A 67 -1 N VAL A 66 O VAL A 31 SHEET 1 B 3 SER A 22 VAL A 25 0 SHEET 2 B 3 VAL A 87 VAL A 92 1 N VAL A 89 O LEU A 23 SHEET 3 B 3 GLY A 72 LYS A 77 -1 N VAL A 76 O GLY A 88
LINK CU CU A 125 ND1 HIS A 40 1555 1555 1.95 LINK CU CU A 125 SG CYS A 78 1555 1555 2.13 LINK CU CU A 125 ND1 HIS A 81 1555 1555 1.92 LINK CU CU A 125 SD MET A 86 1555 1555 2.71
CISPEP 1 GLU A 19 PRO A 20 0 0.06
SITE 1 COP 4 HIS A 40 CYS A 78 HIS A 81 MET A 86 SITE 1 AC1 4 HIS A 40 CYS A 78 HIS A 81 MET A 86
CRYST1 56.731 61.544 30.083 90.00 90.00 90.00 P 21 21 21 4
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 0.017627 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016249 0.000000 0.00000
SCALE3 0.000000 0.000000 0.033241 0.00000