HEADER ELECTRON TRANSPORT 15-SEP-06 2IDT TITLE STRUCTURE OF M98Q MUTANT OF AMICYANIN, CU(II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMICYANIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARACOCCUS DENITRIFICANS; SOURCE 3 ORGANISM_TAXID: 266; SOURCE 4 GENE: MAUC, AMI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMEG KEYWDS BLUE COPPER PROTEIN; BETA SANDWICH, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.J.CARRELL,J.K.MA,W.ANTHOLINE,J.P.HOSLER,F.S.MATHEWS,V.L.DAVIDSON REVDAT 5 30-AUG-23 2IDT 1 REMARK REVDAT 4 20-OCT-21 2IDT 1 REMARK SEQADV LINK REVDAT 3 18-OCT-17 2IDT 1 REMARK REVDAT 2 24-FEB-09 2IDT 1 VERSN REVDAT 1 13-MAR-07 2IDT 0 JRNL AUTH C.J.CARRELL,J.K.MA,W.E.ANTHOLINE,J.P.HOSLER,F.S.MATHEWS, JRNL AUTH 2 V.L.DAVIDSON JRNL TITL GENERATION OF NOVEL COPPER SITES BY MUTATION OF THE AXIAL JRNL TITL 2 LIGAND OF AMICYANIN. ATOMIC RESOLUTION STRUCTURES AND JRNL TITL 3 SPECTROSCOPIC PROPERTIES JRNL REF BIOCHEMISTRY V. 46 1900 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17295442 JRNL DOI 10.1021/BI0619674 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 78.2 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) : 0.126 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.124 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1761 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 35183 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.125 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.124 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1721 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 34434 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 809 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 985.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 8914 REMARK 3 NUMBER OF RESTRAINTS : 10558 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.033 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.032 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.101 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.107 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.018 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.040 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.081 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY ? REMARK 4 REMARK 4 2IDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039458. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 8-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : GE(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35092 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 77.7 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 38.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.09300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: PDB ENTRY 1AAC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.6 M PHOSPHATE, PH 5.5, EVAPORATION, REMARK 280 TEMPERATURE 293K 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 27.74000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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: 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 MET A 28 CB - CG - SD ANGL. DEV. = 21.9 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 VAL A 61 -65.63 -97.79 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 107 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 53 ND1 REMARK 620 2 CYS A 92 SG 130.6 REMARK 620 3 HIS A 95 ND1 104.1 112.8 REMARK 620 4 GLN A 98 OE1 92.7 108.2 104.1 REMARK 620 5 GLN A 98 OE1 96.5 107.8 99.9 5.0 REMARK 620 N 1 2 3 4 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 107 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IDQ RELATED DB: PDB REMARK 900 RELATED ID: 2IDS RELATED DB: PDB REMARK 900 RELATED ID: 2IDU RELATED DB: PDB DBREF 2IDT A 1 105 UNP P22364 AMCY_PARDE 27 131 SEQADV 2IDT MHO A 51 UNP P22364 MET 77 MODIFIED RESIDUE SEQADV 2IDT GLN A 98 UNP P22364 MET 124 ENGINEERED MUTATION SEQRES 1 A 105 ASP LYS ALA THR ILE PRO SER GLU SER PRO PHE ALA ALA SEQRES 2 A 105 ALA GLU VAL ALA ASP GLY ALA ILE VAL VAL ASP ILE ALA SEQRES 3 A 105 LYS MET LYS TYR GLU THR PRO GLU LEU HIS VAL LYS VAL SEQRES 4 A 105 GLY ASP THR VAL THR TRP ILE ASN ARG GLU ALA MHO PRO SEQRES 5 A 105 HIS ASN VAL HIS PHE VAL ALA GLY VAL LEU GLY GLU ALA SEQRES 6 A 105 ALA LEU LYS GLY PRO MET MET LYS LYS GLU GLN ALA TYR SEQRES 7 A 105 SER LEU THR PHE THR GLU ALA GLY THR TYR ASP TYR HIS SEQRES 8 A 105 CYS THR PRO HIS PRO PHE GLN ARG GLY LYS VAL VAL VAL SEQRES 9 A 105 GLU MODRES 2IDT MHO A 51 MET S-OXYMETHIONINE HET MHO A 51 9 HET CU A 107 1 HETNAM MHO S-OXYMETHIONINE HETNAM CU COPPER (II) ION FORMUL 1 MHO C5 H11 N O3 S FORMUL 2 CU CU 2+ FORMUL 3 HOH *175(H2 O) HELIX 1 1 ALA A 14 VAL A 16 5 3 SHEET 1 A 3 ALA A 3 THR A 4 0 SHEET 2 A 3 GLN A 76 PHE A 82 -1 O THR A 81 N THR A 4 SHEET 3 A 3 PHE A 11 ALA A 12 -1 N PHE A 11 O ALA A 77 SHEET 1 B 5 ALA A 3 THR A 4 0 SHEET 2 B 5 GLN A 76 PHE A 82 -1 O THR A 81 N THR A 4 SHEET 3 B 5 THR A 42 ASN A 47 -1 N VAL A 43 O LEU A 80 SHEET 4 B 5 ILE A 21 ALA A 26 1 N ILE A 21 O THR A 42 SHEET 5 B 5 LYS A 29 TYR A 30 -1 O LYS A 29 N ALA A 26 SHEET 1 C 3 GLU A 34 VAL A 37 0 SHEET 2 C 3 ARG A 99 VAL A 104 1 O VAL A 103 N LEU A 35 SHEET 3 C 3 GLY A 86 HIS A 91 -1 N TYR A 88 O VAL A 102 SHEET 1 D 2 HIS A 56 PHE A 57 0 SHEET 2 D 2 LEU A 67 LYS A 68 -1 O LEU A 67 N PHE A 57 LINK C ALA A 50 N MHO A 51 1555 1555 1.34 LINK C MHO A 51 N PRO A 52 1555 1555 1.31 LINK ND1 HIS A 53 CU CU A 107 1555 1555 1.98 LINK SG CYS A 92 CU CU A 107 1555 1555 2.16 LINK ND1 HIS A 95 CU CU A 107 1555 1555 2.02 LINK OE1AGLN A 98 CU CU A 107 1555 1555 2.43 LINK OE1BGLN A 98 CU CU A 107 1555 1555 2.12 SITE 1 AC1 4 HIS A 53 CYS A 92 HIS A 95 GLN A 98 CRYST1 28.410 55.480 27.040 90.00 95.17 90.00 P 1 21 1 2 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 0.035199 0.000000 0.003185 0.00000 SCALE2 0.000000 0.018025 0.000000 0.00000 SCALE3 0.000000 0.000000 0.037133 0.00000