PDB Short entry for 3PAZ HEADER ELECTRON TRANSFER 20-FEB-97 3PAZ TITLE REDUCED NATIVE PSEUDOAZURIN FROM A. FAECALIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PSEUDOAZURIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALCALIGENES FAECALIS; SOURCE 3 ORGANISM_TAXID: 511; SOURCE 4 STRAIN: S-6; SOURCE 5 CELLULAR_LOCATION: PERIPLASM; SOURCE 6 GENE: POTENTIAL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: TG1; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ELECTRON TRANSFER, CUPROPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.T.ADMAN,C.A.P.LIBEU REVDAT 6 21-FEB-24 3PAZ 1 REMARK LINK REVDAT 5 29-NOV-17 3PAZ 1 HELIX REVDAT 4 24-FEB-09 3PAZ 1 VERSN REVDAT 3 01-APR-03 3PAZ 1 JRNL REVDAT 2 22-DEC-99 3PAZ 3 ATOM FORMUL REMARK REVDAT 1 20-AUG-97 3PAZ 0 JRNL AUTH C.A.LIBEU,M.KUKIMOTO,M.NISHIYAMA,S.HORINOUCHI,E.T.ADMAN JRNL TITL SITE-DIRECTED MUTANTS OF PSEUDOAZURIN: EXPLANATION OF JRNL TITL 2 INCREASED REDOX POTENTIALS FROM X-RAY STRUCTURES AND FROM JRNL TITL 3 CALCULATION OF REDOX POTENTIAL DIFFERENCES. JRNL REF BIOCHEMISTRY V. 36 13160 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9341204 JRNL DOI 10.1021/BI9704111 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.NISHIYAMA,J.SUZUKI,T.OHNUKI,H.C.CHANG,S.HORINOUCHI, REMARK 1 AUTH 2 S.TURLEY,E.T.ADMAN,T.BEPPU REMARK 1 TITL SITE-DIRECTED MUTAGENESIS OF PSEUDOAZURIN FROM ALCALIGENES REMARK 1 TITL 2 FAECALIS S-6; PRO80ALA MUTANT EXHIBITS MARKED INCREASE IN REMARK 1 TITL 3 REDUCTION POTENTIAL REMARK 1 REF PROTEIN ENG. V. 5 177 1992 REMARK 1 REFN ISSN 0269-2139 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.T.ADMAN,S.TURLEY,R.BRAMSON,K.PETRATOS,D.BANNER, REMARK 1 AUTH 2 D.TSERNOGLOU,T.BEPPU,H.WATANABE REMARK 1 TITL A 2.0-A STRUCTURE OF THE BLUE COPPER PROTEIN (CUPREDOXIN) REMARK 1 TITL 2 FROM ALCALIGENES FAECALIS S-6 REMARK 1 REF J.BIOL.CHEM. V. 264 87 1989 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.164 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.164 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 12699 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.157 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.157 REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 11505 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 933 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 90 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 6 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4279 REMARK 3 NUMBER OF RESTRAINTS : 3997 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 ANGLE DISTANCES (A) : 0.020 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.163 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.088 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.107 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.022 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.012 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.040 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: BABINET'S PRINCIPLE (SHELX-93) REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: COPPER-LIGAND DISTANCES NOT RESTRAINED; REMARK 3 CU + S REFINED ANISOTROPICALLY REMARK 4 REMARK 4 3PAZ 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_1000179083. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : DEC-93 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 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 : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12220 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 22.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.15000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM SODIUM PHOSPHATE WITH 75% REMARK 280 SATURATED AMMONIUM SULFATE, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.81333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.90667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.36000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 16.45333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 82.26667 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 46 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TYR A 74 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 81.56 57.24 REMARK 500 GLU A 51 -56.86 -27.19 REMARK 500 ASN A 61 -5.60 78.19 REMARK 500 SER A 95 71.87 30.29 REMARK 500 SER A 121 66.89 -108.36 REMARK 500 ALA A 122 -17.04 172.38 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 124 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 40 ND1 REMARK 620 2 CYS A 78 SG 142.8 REMARK 620 3 HIS A 81 ND1 98.3 105.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CU REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ACTIVE SITE FOR ELECTRON TRANSFER. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 124 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PAZ RELATED DB: PDB REMARK 900 RELATED ID: 5PAZ RELATED DB: PDB REMARK 900 RELATED ID: 6PAZ RELATED DB: PDB REMARK 900 RELATED ID: 7PAZ RELATED DB: PDB REMARK 900 RELATED ID: 8PAZ RELATED DB: PDB DBREF 3PAZ A 1 123 UNP P04377 AZUP_ALCFA 24 146 SEQRES 1 A 123 GLU ASN ILE GLU VAL HIS MET LEU ASN LYS GLY ALA GLU SEQRES 2 A 123 GLY ALA MET VAL PHE GLU PRO ALA TYR ILE LYS ALA ASN SEQRES 3 A 123 PRO GLY ASP THR VAL THR PHE ILE PRO VAL ASP LYS GLY SEQRES 4 A 123 HIS ASN VAL GLU SER ILE LYS ASP MET ILE PRO GLU GLY SEQRES 5 A 123 ALA GLU LYS PHE LYS SER LYS ILE ASN GLU ASN TYR VAL SEQRES 6 A 123 LEU THR VAL THR GLN PRO GLY ALA TYR LEU VAL LYS CYS SEQRES 7 A 123 THR PRO HIS TYR ALA MET GLY MET ILE ALA LEU ILE ALA SEQRES 8 A 123 VAL GLY ASP SER PRO ALA ASN LEU ASP GLN ILE VAL SER SEQRES 9 A 123 ALA LYS LYS PRO LYS ILE VAL GLN GLU ARG LEU GLU LYS SEQRES 10 A 123 VAL ILE ALA SER ALA LYS HET CU A 124 1 HETNAM CU COPPER (II) ION FORMUL 2 CU CU 2+ FORMUL 3 HOH *90(H2 O) HELIX 1 1 TYR A 82 MET A 84 5 3 HELIX 2 2 LEU A 99 VAL A 103 1 5 HELIX 3 3 LYS A 109 ALA A 120 1 12 SHEET 1 A 4 VAL A 17 GLU A 19 0 SHEET 2 A 4 ASN 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 ILE A 3 SHEET 4 A 4 TYR A 64 THR A 67 -1 N LEU A 66 O VAL A 31 SHEET 1 B 3 TYR A 22 ALA A 25 0 SHEET 2 B 3 ILE A 87 VAL A 92 1 N LEU A 89 O ILE A 23 SHEET 3 B 3 GLY A 72 LYS A 77 -1 N VAL A 76 O ALA A 88 LINK ND1 HIS A 40 CU CU A 124 1555 1555 2.10 LINK SG CYS A 78 CU CU A 124 1555 1555 2.17 LINK ND1 HIS A 81 CU CU A 124 1555 1555 2.31 CISPEP 1 GLU A 19 PRO A 20 0 -0.03 SITE 1 CU 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 50.060 50.060 98.720 90.00 90.00 120.00 P 65 6 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 0.019976 0.011533 0.000000 0.00000 SCALE2 0.000000 0.023066 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010130 0.00000