HEADER ELECTRON TRANSPORT 06-SEP-97 1NWO TITLE CRYSTALLOGRAPHIC STUDY OF AZURIN FROM PSEUDOMONAS PUTIDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: AZURIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 STRAIN: NCIB 9869 KEYWDS ELECTRON TRANSPORT, CUPREDOXIN, ELECTRON TRANSFER EXPDTA X-RAY DIFFRACTION AUTHOR F.S.MATHEWS,Z.-W.CHEN REVDAT 4 09-AUG-23 1NWO 1 REMARK LINK REVDAT 3 24-FEB-09 1NWO 1 VERSN REVDAT 2 01-APR-03 1NWO 1 JRNL REVDAT 1 28-JAN-98 1NWO 0 JRNL AUTH Z.W.CHEN,M.J.BARBER,W.S.MCINTIRE,F.S.MATHEWS JRNL TITL CRYSTALLOGRAPHIC STUDY OF AZURIN FROM PSEUDOMONAS PUTIDA. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 54 253 1998 JRNL REFN ISSN 0907-4449 JRNL PMID 9761890 JRNL DOI 10.1107/S0907444997011505 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.J.BARBER,A.J.TRIMBOLI,W.S.MCINTIRE REMARK 1 TITL THE AMINO ACID SEQUENCE OF PSEUDOMONAS PUTIDA AZURIN REMARK 1 REF ARCH.BIOCHEM.BIOPHYS. V. 303 22 1993 REMARK 1 REFN ISSN 0003-9861 REMARK 2 REMARK 2 RESOLUTION. 1.92 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 15329 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.300 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL 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) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 46.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 738 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1916 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 163 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.90 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) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.020 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.730 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.360 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.660 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NWO 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_1000175405. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : SEP-90 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.5-7.5 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : CU KA RADIATION REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XUONG-HAMLIN MULTIWIRE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAME AS ABOVE, HAMLIN REMARK 200 DATA SCALING SOFTWARE : HAMLIN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16127 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 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 (%) : 92.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.19300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: AZURIN FROM ALCALIGENES DENITRIFICANS (PDB ENTRY REMARK 200 2AZA) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP METHOD AT 4 C BY MIXING 5 REMARK 280 MICRLITER PROTEIN AT 10- 15MG PER ML WITH 5 MICROLITER 30-36% REMARK 280 PEG8000 SOLUTION CONTAINING 5MM TRIS-HCL BUFFER, PH 6.5-7.5 AND REMARK 280 100MM NACL., VAPOR DIFFUSION - HANGING DROP, TEMPERATURE 277K, REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 25.32500 REMARK 290 SMTRY3 2 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 44 49.05 -143.98 REMARK 500 MET B 44 55.53 -141.87 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 199 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 46 ND1 REMARK 620 2 CYS A 112 SG 131.9 REMARK 620 3 HIS A 117 ND1 106.6 118.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 199 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 46 ND1 REMARK 620 2 CYS B 112 SG 131.4 REMARK 620 3 HIS B 117 ND1 102.5 124.8 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 199 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU B 199 DBREF 1NWO A 1 128 UNP P34097 AZUR_PSEPU 1 128 DBREF 1NWO B 1 128 UNP P34097 AZUR_PSEPU 1 128 SEQRES 1 A 128 ALA GLU CYS LYS VAL THR VAL ASP SER THR ASP GLN MET SEQRES 2 A 128 SER PHE ASN THR LYS ASP ILE ALA ILE ASP LYS SER CYS SEQRES 3 A 128 LYS THR PHE THR VAL GLU LEU THR HIS SER GLY SER LEU SEQRES 4 A 128 PRO LYS ASN VAL MET GLY HIS ASN LEU VAL ILE SER LYS SEQRES 5 A 128 GLU ALA ASP MET GLN PRO ILE ALA THR ASP GLY LEU SER SEQRES 6 A 128 ALA GLY ILE ASP LYS GLN TYR LEU LYS ASP GLY ASP ALA SEQRES 7 A 128 ARG VAL ILE ALA HIS THR LYS VAL ILE GLY ALA GLY GLU SEQRES 8 A 128 LYS ASP SER VAL THR PHE ASP VAL SER LYS LEU ALA ALA SEQRES 9 A 128 GLY GLU LYS TYR GLY PHE PHE CYS SER PHE PRO GLY HIS SEQRES 10 A 128 ILE SER MET MET LYS GLY THR VAL THR LEU LYS SEQRES 1 B 128 ALA GLU CYS LYS VAL THR VAL ASP SER THR ASP GLN MET SEQRES 2 B 128 SER PHE ASN THR LYS ASP ILE ALA ILE ASP LYS SER CYS SEQRES 3 B 128 LYS THR PHE THR VAL GLU LEU THR HIS SER GLY SER LEU SEQRES 4 B 128 PRO LYS ASN VAL MET GLY HIS ASN LEU VAL ILE SER LYS SEQRES 5 B 128 GLU ALA ASP MET GLN PRO ILE ALA THR ASP GLY LEU SER SEQRES 6 B 128 ALA GLY ILE ASP LYS GLN TYR LEU LYS ASP GLY ASP ALA SEQRES 7 B 128 ARG VAL ILE ALA HIS THR LYS VAL ILE GLY ALA GLY GLU SEQRES 8 B 128 LYS ASP SER VAL THR PHE ASP VAL SER LYS LEU ALA ALA SEQRES 9 B 128 GLY GLU LYS TYR GLY PHE PHE CYS SER PHE PRO GLY HIS SEQRES 10 B 128 ILE SER MET MET LYS GLY THR VAL THR LEU LYS HET CU A 199 1 HET CU B 199 1 HETNAM CU COPPER (II) ION FORMUL 3 CU 2(CU 2+) FORMUL 5 HOH *163(H2 O) HELIX 1 A1 GLU A 53 ALA A 66 1 14 HELIX 2 A2 ASP A 98 LEU A 102 5 5 HELIX 3 B1 GLU B 53 SER B 65 1 13 HELIX 4 B2 ASP B 98 LEU B 102 5 5 SHEET 1 A1 4 SER A 14 ASN A 16 0 SHEET 2 A1 4 CYS A 3 THR A 10 -1 SHEET 3 A1 4 LYS A 27 SER A 36 1 SHEET 4 A1 4 GLY A 90 VAL A 99 -1 SHEET 1 A2 5 LYS A 18 LYS A 24 0 SHEET 2 A2 5 MET A 121 LYS A 128 1 SHEET 3 A2 5 LYS A 107 CYS A 112 -1 SHEET 4 A2 5 HIS A 46 GLU A 53 -1 SHEET 5 A2 5 ILE A 81 ILE A 87 -1 SHEET 1 B1 4 SER B 14 ASN B 16 0 SHEET 2 B1 4 CYS B 3 THR B 10 -1 SHEET 3 B1 4 LYS B 27 SER B 36 1 SHEET 4 B1 4 GLY B 90 VAL B 99 -1 SHEET 1 B2 5 LYS B 18 LYS B 24 0 SHEET 2 B2 5 MET B 121 LYS B 128 1 SHEET 3 B2 5 LYS B 107 CYS B 112 -1 SHEET 4 B2 5 HIS B 46 GLU B 53 -1 SHEET 5 B2 5 ILE B 81 ILE B 87 -1 SSBOND 1 CYS A 3 CYS A 26 1555 1555 2.03 SSBOND 2 CYS B 3 CYS B 26 1555 1555 2.02 LINK ND1 HIS A 46 CU CU A 199 1555 1555 2.01 LINK SG CYS A 112 CU CU A 199 1555 1555 2.13 LINK ND1 HIS A 117 CU CU A 199 1555 1555 1.94 LINK ND1 HIS B 46 CU CU B 199 1555 1555 1.93 LINK SG CYS B 112 CU CU B 199 1555 1555 2.14 LINK ND1 HIS B 117 CU CU B 199 1555 1555 1.96 SITE 1 AC1 5 GLY A 45 HIS A 46 CYS A 112 HIS A 117 SITE 2 AC1 5 MET A 121 SITE 1 AC2 5 GLY B 45 HIS B 46 CYS B 112 HIS B 117 SITE 2 AC2 5 MET B 121 CRYST1 43.250 50.650 54.600 90.00 107.79 90.00 P 1 21 1 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 0.023121 0.000000 0.007419 0.00000 SCALE2 0.000000 0.019743 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019235 0.00000