HEADER ELECTRON TRANSPORT 17-AUG-98 1BQR TITLE REDUCED PSEUDOAZURIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSEUDOAZURIN; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: REDUCED BY ASCORBIC ACID SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACHROMOBACTER CYCLOCLASTES; SOURCE 3 ORGANISM_TAXID: 223; SOURCE 4 STRAIN: IAM1013 KEYWDS ELECTRON TRANSPORT, CUPROPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.INOUE,N.NISHIO,S.HAMANAKA,T.SHIMOMURA,S.HARADA,S.SUZUKI,T.KOHZUMA, AUTHOR 2 S.SHIDARA,H.IWASAKI,Y.KAI REVDAT 4 22-MAY-24 1BQR 1 REMARK REVDAT 3 09-AUG-23 1BQR 1 REMARK LINK REVDAT 2 24-FEB-09 1BQR 1 VERSN REVDAT 1 17-AUG-99 1BQR 0 JRNL AUTH T.INOUE,N.NISHIO,S.SUZUKI,K.KATAOKA,T.KOHZUMA,Y.KAI JRNL TITL CRYSTAL STRUCTURE DETERMINATIONS OF OXIDIZED AND REDUCED JRNL TITL 2 PSEUDOAZURINS FROM ACHROMOBACTER CYCLOCLASTES. CONCERTED JRNL TITL 3 MOVEMENT OF COPPER SITE IN REDOX FORMS WITH THE JRNL TITL 4 REARRANGEMENT OF HYDROGEN 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 REDUCED REMARK 1 TITL 2 PSEUDOAZURIN FROM ACHROMOBACTER CYCLOCLASTES: A REMARK 1 TITL 3 REDOX-INDUCED CONFORMATIONAL CHANGE CONTAINS A PEPTIDE BOND REMARK 1 TITL 4 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 IAM1013 REMARK 1 REF J.BIOCHEM.(TOKYO) V. 114 761 1993 REMARK 1 REFN ISSN 0021-924X REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 3 NUMBER OF REFLECTIONS : 12449 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 680 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 : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.20 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) : 0.010 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.026 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.030 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.024 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.138 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.173 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.244 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.140 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 10.600; 15.000 REMARK 3 PLANAR (DEGREES) : 4.200 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 16.800; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 22.400; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.414 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.094 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.224 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.469 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ESTIMATED COORDINATE ERROR. ESD FROM REMARK 3 LUZZATI PLOT (A) : 0.153 REMARK 4 REMARK 4 1BQR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172010. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13287 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.14100 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: MERLOT REMARK 200 STARTING MODEL: PDB ENTRY 1PZA REMARK 200 REMARK 200 REMARK: NULL 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 28.32500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.21000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.83500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 15.21000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.32500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.83500 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 78.29 57.99 REMARK 500 THR A 69 -64.93 -101.30 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 CU A 125 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 40 ND1 REMARK 620 2 CYS A 78 SG 132.2 REMARK 620 3 HIS A 81 ND1 101.8 116.3 REMARK 620 4 MET A 86 SD 89.5 107.1 103.7 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: REDUCED COPPER COORDINATION REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 125 DBREF 1BQR 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 *96(H2 O) HELIX 1 1 TYR A 82 MET A 84 5 3 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 PRO A 35 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 ND1 HIS A 40 CU CU A 125 1555 1555 2.04 LINK SG CYS A 78 CU CU A 125 1555 1555 2.19 LINK ND1 HIS A 81 CU CU A 125 1555 1555 2.11 LINK SD MET A 86 CU CU A 125 1555 1555 2.86 CISPEP 1 GLU A 19 PRO A 20 0 -1.91 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 56.650 61.670 30.420 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 0.017652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016215 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032873 0.00000