HEADER ELECTRON TRANSPORT 18-FEB-97 1ADW TITLE PSEUDOAZURIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSEUDOAZURIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARACOCCUS PANTOTROPHUS; SOURCE 3 ORGANISM_TAXID: 82367; SOURCE 4 STRAIN: GB17; SOURCE 5 ATCC: 35512; SOURCE 6 CELLULAR_LOCATION: PERIPLASM KEYWDS COPPER, ELECTRON TRANSPORT, CUPROPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.A.WILLIAMS REVDAT 4 02-AUG-23 1ADW 1 REMARK LINK REVDAT 3 24-FEB-09 1ADW 1 VERSN REVDAT 2 30-SEP-03 1ADW 1 DBREF REVDAT 1 15-MAY-97 1ADW 0 JRNL AUTH P.A.WILLIAMS,V.FULOP,Y.C.LEUNG,C.CHAN,J.W.MOIR,G.HOWLETT, JRNL AUTH 2 S.J.FERGUSON,S.E.RADFORD,J.HAJDU JRNL TITL PSEUDOSPECIFIC DOCKING SURFACES ON ELECTRON TRANSFER JRNL TITL 2 PROTEINS AS ILLUSTRATED BY PSEUDOAZURIN, CYTOCHROME C550 AND JRNL TITL 3 CYTOCHROME CD1 NITRITE REDUCTASE. JRNL REF NAT.STRUCT.BIOL. V. 2 975 1995 JRNL REFN ISSN 1072-8368 JRNL PMID 7583671 JRNL DOI 10.1038/NSB1195-975 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0100 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 10531 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 SET) : 0.189 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 402 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.60 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.44 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 979 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 2.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 40 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1868 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 56 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.30 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : 0.40 REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.380 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 2.500 REMARK 3 REMARK 3 NCS MODEL : RESTRAINED REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARCHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM11.WAT REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19.PEP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ADW 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_1000170697. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-94 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.0 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10531 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10700 REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34400 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: PDB ENTRY 2PAZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2 M AMMONIUM SULFATE 50MM POTASSIUM REMARK 280 PHOSPHATE PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 55.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.00000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.20000 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: DIMERIC 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 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 75.16 53.48 REMARK 500 SER A 39 4.70 93.65 REMARK 500 ILE A 48 72.00 -110.51 REMARK 500 ALA A 95 76.75 35.95 REMARK 500 MET B 16 76.15 51.50 REMARK 500 SER B 39 2.06 95.15 REMARK 500 ILE B 48 72.93 -111.48 REMARK 500 ALA B 95 76.34 35.08 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 130 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 40 ND1 REMARK 620 2 CYS A 78 SG 136.6 REMARK 620 3 HIS A 81 ND1 100.6 111.2 REMARK 620 4 MET A 86 SD 81.9 113.4 108.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 130 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 40 ND1 REMARK 620 2 CYS B 78 SG 135.4 REMARK 620 3 HIS B 81 ND1 99.9 110.7 REMARK 620 4 MET B 86 SD 82.9 114.1 109.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CUA REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CU BINDING SITE - HIS 40, CYS 78, HIS 81, AND REMARK 800 MET 86 ARE LIGANDS TO THE COPPER. REMARK 800 REMARK 800 SITE_IDENTIFIER: CUB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CU BINDING SITE - HIS 40, CYS 78, HIS 81, AND REMARK 800 MET 86 ARE LIGANDS TO THE COPPER. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 130 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU B 130 DBREF 1ADW A 1 123 UNP P80401 AZUP_PARPN 23 145 DBREF 1ADW B 1 123 UNP P80401 AZUP_PARPN 23 145 SEQRES 1 A 123 ALA THR HIS GLU VAL HIS MET LEU ASN LYS GLY GLU SER SEQRES 2 A 123 GLY ALA MET VAL PHE GLU PRO ALA PHE VAL ARG ALA GLU SEQRES 3 A 123 PRO GLY ASP VAL ILE ASN PHE VAL PRO THR ASP LYS SER SEQRES 4 A 123 HIS ASN VAL GLU ALA ILE LYS GLU ILE LEU PRO GLU GLY SEQRES 5 A 123 VAL GLU SER PHE LYS SER LYS ILE ASN GLU SER TYR THR SEQRES 6 A 123 LEU THR VAL THR GLU PRO GLY LEU TYR GLY VAL LYS CYS SEQRES 7 A 123 THR PRO HIS PHE GLY MET GLY MET VAL GLY LEU VAL GLN SEQRES 8 A 123 VAL GLY ASP ALA PRO GLU ASN LEU ASP ALA ALA LYS THR SEQRES 9 A 123 ALA LYS MET PRO LYS LYS ALA ARG GLU ARG MET ASP ALA SEQRES 10 A 123 GLU LEU ALA GLN VAL ASN SEQRES 1 B 123 ALA THR HIS GLU VAL HIS MET LEU ASN LYS GLY GLU SER SEQRES 2 B 123 GLY ALA MET VAL PHE GLU PRO ALA PHE VAL ARG ALA GLU SEQRES 3 B 123 PRO GLY ASP VAL ILE ASN PHE VAL PRO THR ASP LYS SER SEQRES 4 B 123 HIS ASN VAL GLU ALA ILE LYS GLU ILE LEU PRO GLU GLY SEQRES 5 B 123 VAL GLU SER PHE LYS SER LYS ILE ASN GLU SER TYR THR SEQRES 6 B 123 LEU THR VAL THR GLU PRO GLY LEU TYR GLY VAL LYS CYS SEQRES 7 B 123 THR PRO HIS PHE GLY MET GLY MET VAL GLY LEU VAL GLN SEQRES 8 B 123 VAL GLY ASP ALA PRO GLU ASN LEU ASP ALA ALA LYS THR SEQRES 9 B 123 ALA LYS MET PRO LYS LYS ALA ARG GLU ARG MET ASP ALA SEQRES 10 B 123 GLU LEU ALA GLN VAL ASN HET CU A 130 1 HET CU B 130 1 HETNAM CU COPPER (II) ION FORMUL 3 CU 2(CU 2+) FORMUL 5 HOH *56(H2 O) HELIX 1 1 THR A 79 HIS A 81 5 3 HELIX 2 2 LEU A 99 THR A 104 1 6 HELIX 3 3 LYS A 109 GLN A 121 1 13 HELIX 4 4 THR B 79 HIS B 81 5 3 HELIX 5 5 LEU B 99 THR B 104 1 6 HELIX 6 6 LYS B 109 GLN B 121 1 13 SHEET 1 A 4 VAL A 17 GLU A 19 0 SHEET 2 A 4 THR A 2 LEU A 8 -1 N LEU A 8 O VAL A 17 SHEET 3 A 4 ASP A 29 PRO A 35 1 N VAL A 30 O HIS A 3 SHEET 4 A 4 TYR A 64 VAL A 68 -1 N VAL A 68 O ASP A 29 SHEET 1 B 3 PHE A 22 ALA A 25 0 SHEET 2 B 3 VAL A 87 VAL A 92 1 N LEU A 89 O VAL A 23 SHEET 3 B 3 GLY A 72 LYS A 77 -1 N VAL A 76 O GLY A 88 SHEET 1 C 4 VAL B 17 GLU B 19 0 SHEET 2 C 4 THR B 2 LEU B 8 -1 N LEU B 8 O VAL B 17 SHEET 3 C 4 ASP B 29 PRO B 35 1 N VAL B 30 O HIS B 3 SHEET 4 C 4 TYR B 64 VAL B 68 -1 N VAL B 68 O ASP B 29 SHEET 1 D 3 PHE B 22 ALA B 25 0 SHEET 2 D 3 VAL B 87 VAL B 92 1 N LEU B 89 O VAL B 23 SHEET 3 D 3 GLY B 72 LYS B 77 -1 N VAL B 76 O GLY B 88 LINK ND1 HIS A 40 CU CU A 130 1555 1555 2.13 LINK SG CYS A 78 CU CU A 130 1555 1555 2.13 LINK ND1 HIS A 81 CU CU A 130 1555 1555 2.11 LINK SD MET A 86 CU CU A 130 1555 1555 2.75 LINK ND1 HIS B 40 CU CU B 130 1555 1555 2.12 LINK SG CYS B 78 CU CU B 130 1555 1555 2.14 LINK ND1 HIS B 81 CU CU B 130 1555 1555 2.15 LINK SD MET B 86 CU CU B 130 1555 1555 2.70 CISPEP 1 GLU A 19 PRO A 20 0 -0.22 CISPEP 2 GLU B 19 PRO B 20 0 0.14 SITE 1 CUA 1 CU A 130 SITE 1 CUB 1 CU B 130 SITE 1 AC1 4 HIS A 40 CYS A 78 HIS A 81 MET A 86 SITE 1 AC2 4 HIS B 40 CYS B 78 HIS B 81 MET B 86 CRYST1 110.000 58.400 69.200 90.00 127.00 90.00 C 1 2 1 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 0.009091 0.000000 0.006850 0.00000 SCALE2 0.000000 0.017123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018094 0.00000 MTRIX1 1 0.282686 0.028475 0.958790 -42.56462 1 MTRIX2 1 0.039845 -0.999045 0.017923 -1.73786 1 MTRIX3 1 0.958385 0.033137 -0.283550 56.79548 1