HEADER ELECTRON TRANSPORT 11-AUG-09 3IN2 TITLE CRYSTAL STRUCTURE OF THE N47S/M121L VARIANT OF PSEUDOMONAS AERUGINOSA TITLE 2 AZURIN IN THE CU(II) STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AZURIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: N47S/M121L VARIANT OF AZURIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: AZU, PA4922; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET9A KEYWDS CUPREDOXIN, AZURIN, GREEK KEY, BETA BARREL, ELECTRON TRANSFER, KEYWDS 2 COPPER, DISULFIDE BOND, ELECTRON TRANSPORT, METAL-BINDING, KEYWDS 3 PERIPLASM, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Y.G.GAO,H.ROBINSON REVDAT 2 13-OCT-21 3IN2 1 REMARK SEQADV REVDAT 1 17-NOV-09 3IN2 0 JRNL AUTH N.M.MARSHALL,D.K.GARNER,T.D.WILSON,Y.G.GAO,H.ROBINSON, JRNL AUTH 2 M.J.NILGES,Y.LU JRNL TITL RATIONALLY TUNING THE REDUCTION POTENTIAL OF A SINGLE JRNL TITL 2 CUPREDOXIN BEYOND THE NATURAL RANGE. JRNL REF NATURE V. 462 113 2009 JRNL REFN ISSN 0028-0836 JRNL PMID 19890331 JRNL DOI 10.1038/NATURE08551 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.238 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.238 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 4005 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.238 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 0.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 3739 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 971 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1057.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3270 REMARK 3 NUMBER OF RESTRAINTS : 4062 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 ANGLE DISTANCES (A) : 1.560 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.018 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.015 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.025 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.005 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.091 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 REMARK 4 REMARK 4 3IN2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054616. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : CRYOGENICALLY COOLED DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR WITH REMARK 200 HORIZONTALLY FOCUSING SAGITALLY REMARK 200 BENT SECOND MONO CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4005 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 22.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, 0.08M NAOAC, 0.2M LITHIUM REMARK 280 NITRATE, 0.2M CALCIUM CHLORIDE, PH 6.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 52.55000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.83000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.83000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 78.82500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.83000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.83000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.27500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.83000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.83000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 78.82500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.83000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.83000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.27500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 52.55000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 CYS A 3 49.74 20.53 REMARK 500 GLN A 12 35.26 -84.31 REMARK 500 MET A 13 43.88 31.52 REMARK 500 ALA A 19 151.47 172.27 REMARK 500 GLN A 28 104.91 166.38 REMARK 500 MET A 44 56.58 -170.24 REMARK 500 THR A 52 174.08 -49.99 REMARK 500 VAL A 60 -72.90 -68.77 REMARK 500 ILE A 87 -164.78 -77.48 REMARK 500 SER A 89 112.89 -28.97 REMARK 500 VAL A 95 144.38 174.99 REMARK 500 PRO A 115 89.90 -25.23 REMARK 500 LYS A 122 -179.51 -174.42 REMARK 500 LEU A 127 58.84 -116.72 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 201 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 45 O REMARK 620 2 HIS A 46 ND1 65.0 REMARK 620 3 HIS A 117 ND1 81.1 106.7 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 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IN0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF F114P/M121Q VARIANT OF PSEUDOMONAS AERUGINOSA REMARK 900 AZURIN IN THE CU(II) STATE DBREF 3IN2 A 1 128 UNP P00282 AZUR_PSEAE 21 148 SEQADV 3IN2 SER A 47 UNP P00282 ASN 67 ENGINEERED MUTATION SEQADV 3IN2 LEU A 121 UNP P00282 MET 141 ENGINEERED MUTATION SEQRES 1 A 128 ALA GLU CYS SER VAL ASP ILE GLN GLY ASN ASP GLN MET SEQRES 2 A 128 GLN PHE ASN THR ASN ALA ILE THR VAL ASP LYS SER CYS SEQRES 3 A 128 LYS GLN PHE THR VAL ASN LEU SER HIS PRO GLY ASN LEU SEQRES 4 A 128 PRO LYS ASN VAL MET GLY HIS SER TRP VAL LEU SER THR SEQRES 5 A 128 ALA ALA ASP MET GLN GLY VAL VAL THR ASP GLY MET ALA SEQRES 6 A 128 SER GLY LEU ASP LYS ASP TYR LEU LYS PRO ASP ASP SER SEQRES 7 A 128 ARG VAL ILE ALA HIS THR LYS LEU ILE GLY SER GLY GLU SEQRES 8 A 128 LYS ASP SER VAL THR PHE ASP VAL SER LYS LEU LYS GLU SEQRES 9 A 128 GLY GLU GLN TYR MET PHE PHE CYS THR PHE PRO GLY HIS SEQRES 10 A 128 SER ALA LEU LEU LYS GLY THR LEU THR LEU LYS HET CU A 201 1 HETNAM CU COPPER (II) ION FORMUL 2 CU CU 2+ FORMUL 3 HOH *84(H2 O) HELIX 1 1 ASP A 55 ASP A 62 1 8 SHEET 1 A 2 GLY A 9 ASN A 10 0 SHEET 2 A 2 GLN A 14 PHE A 15 -1 O GLN A 14 N ASN A 10 SHEET 1 B 3 ALA A 19 THR A 21 0 SHEET 2 B 3 LYS A 122 THR A 126 1 O THR A 124 N ILE A 20 SHEET 3 B 3 MET A 109 PHE A 111 -1 N PHE A 110 O GLY A 123 SHEET 1 C 2 PHE A 29 THR A 30 0 SHEET 2 C 2 THR A 96 PHE A 97 -1 O PHE A 97 N PHE A 29 SHEET 1 D 2 VAL A 49 LEU A 50 0 SHEET 2 D 2 ALA A 82 HIS A 83 -1 O ALA A 82 N LEU A 50 SSBOND 1 CYS A 3 CYS A 26 1555 1555 2.03 LINK O GLY A 45 CU CU A 201 1555 1555 2.12 LINK ND1 HIS A 46 CU CU A 201 1555 1555 1.95 LINK ND1 HIS A 117 CU CU A 201 1555 1555 1.96 SITE 1 AC1 4 GLY A 45 HIS A 46 CYS A 112 HIS A 117 CRYST1 49.660 49.660 105.100 90.00 90.00 90.00 P 43 21 2 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 0.020137 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020137 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009515 0.00000