HEADER ELECTRON TRANSPORT 11-MAY-11 3RYM TITLE STRUCTURE OF OXIDIZED M98K MUTANT OF AMICYANIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMICYANIN; COMPND 3 CHAIN: A, B, C, D; 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: AMI, MAUC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMEG KEYWDS TYPE I BLUE COPPER PROTEIN, BETA SANDWICH, ELECTRON TRANSPORT, METAL KEYWDS 2 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR N.SUKUMAR,V.L.DAVIDSON REVDAT 2 13-SEP-23 3RYM 1 REMARK SEQADV LINK REVDAT 1 23-NOV-11 3RYM 0 JRNL AUTH N.SUKUMAR,M.CHOI,V.L.DAVIDSON JRNL TITL REPLACEMENT OF THE AXIAL COPPER LIGAND METHIONINE WITH JRNL TITL 2 LYSINE IN AMICYANIN CONVERTS IT TO A ZINC-BINDING PROTEIN JRNL TITL 3 THAT NO LONGER BINDS COPPER. JRNL REF J.INORG.BIOCHEM. V. 105 1638 2011 JRNL REFN ISSN 0162-0134 JRNL PMID 22071089 JRNL DOI 10.1016/J.JINORGBIO.2011.08.002 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 39490 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1992 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.2902 - 3.6689 0.97 3751 235 0.1591 0.1800 REMARK 3 2 3.6689 - 2.9129 0.98 3827 196 0.1832 0.2060 REMARK 3 3 2.9129 - 2.5449 0.98 3799 208 0.2129 0.2230 REMARK 3 4 2.5449 - 2.3123 0.97 3810 194 0.2030 0.2457 REMARK 3 5 2.3123 - 2.1466 0.97 3778 205 0.1948 0.2194 REMARK 3 6 2.1466 - 2.0201 0.97 3821 181 0.1898 0.2389 REMARK 3 7 2.0201 - 1.9189 0.96 3735 197 0.1883 0.2398 REMARK 3 8 1.9189 - 1.8354 0.96 3773 205 0.2078 0.2471 REMARK 3 9 1.8354 - 1.7648 0.96 3721 187 0.2031 0.2255 REMARK 3 10 1.7648 - 1.7039 0.89 3483 184 0.2225 0.2553 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 39.84 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.74070 REMARK 3 B22 (A**2) : 1.29430 REMARK 3 B33 (A**2) : 0.44650 REMARK 3 B12 (A**2) : -0.73020 REMARK 3 B13 (A**2) : 0.24100 REMARK 3 B23 (A**2) : 3.03820 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.018 3316 REMARK 3 ANGLE : 1.600 4508 REMARK 3 CHIRALITY : NULL 504 REMARK 3 PLANARITY : 0.010 580 REMARK 3 DIHEDRAL : 11.900 1200 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN 'A' AND (RESSEQ 1:105 ) AND (NOT REMARK 3 ELEMENT H) AND (NOT ELEMENT D) REMARK 3 SELECTION : CHAIN 'B' AND (RESSEQ 1:105 ) AND (NOT REMARK 3 ELEMENT H) AND (NOT ELEMENT D) REMARK 3 ATOM PAIRS NUMBER : 808 REMARK 3 RMSD : 0.836 REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: CHAIN 'A' AND (RESSEQ 1:105 ) AND (NOT REMARK 3 ELEMENT H) AND (NOT ELEMENT D) REMARK 3 SELECTION : CHAIN 'C' AND (RESSEQ 1:105 ) AND (NOT REMARK 3 ELEMENT H) AND (NOT ELEMENT D) REMARK 3 ATOM PAIRS NUMBER : 808 REMARK 3 RMSD : 0.712 REMARK 3 NCS OPERATOR : 3 REMARK 3 REFERENCE SELECTION: CHAIN 'A' AND (RESSEQ 1:105 ) AND (NOT REMARK 3 ELEMENT H) AND (NOT ELEMENT D) REMARK 3 SELECTION : CHAIN 'D' AND (RESSEQ 1:105 ) AND (NOT REMARK 3 ELEMENT H) AND (NOT ELEMENT D) REMARK 3 ATOM PAIRS NUMBER : 808 REMARK 3 RMSD : 0.436 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3RYM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065538. 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 : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : 39551 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : NULL REMARK 200 DATA REDUNDANCY : 2.140 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.31300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.820 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 1AAC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01M ZINC SULPHATE HEPTAHYDRATE, 0.1M REMARK 280 MES PH 6.5, 25% W/V PEG MONOMETHYLETHER 550, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 350 REMARK 350 BIOMOLECULE: 3 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: C 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 350 REMARK 350 BIOMOLECULE: 4 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: D 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP B 18 C ASP B 18 O -0.152 REMARK 500 GLU B 49 CB GLU B 49 CG -0.116 REMARK 500 GLU D 49 CB GLU D 49 CG -0.116 REMARK 500 REMARK 500 REMARK: NULL 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 PHE A 97 O - C - N ANGL. DEV. = -10.4 DEGREES REMARK 500 ASP B 18 O - C - N ANGL. DEV. = -12.4 DEGREES REMARK 500 MET B 71 O - C - N ANGL. DEV. = -10.0 DEGREES REMARK 500 ARG B 99 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG B 99 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ALA D 17 CA - C - O ANGL. DEV. = 15.5 DEGREES REMARK 500 PHE D 97 O - C - N ANGL. DEV. = -9.7 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 LYS B 2 2.94 -54.61 REMARK 500 ALA B 26 175.86 -46.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 MET B 71 -11.07 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 ZN A 107 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 36 ND1 REMARK 620 2 GLU A 105 OE2 112.2 REMARK 620 3 GLU A 105 OE1 92.8 52.9 REMARK 620 4 HIS C 36 ND1 99.6 87.7 140.4 REMARK 620 5 GLU C 105 OE2 95.7 141.2 101.3 114.5 REMARK 620 6 GLU C 105 OE1 149.8 97.4 100.7 87.1 55.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 106 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 53 ND1 REMARK 620 2 CYS A 92 SG 117.7 REMARK 620 3 HIS A 95 ND1 100.8 110.3 REMARK 620 4 LYS A 98 NZ 106.4 115.0 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 107 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 36 ND1 REMARK 620 2 GLU B 105 OE2 119.9 REMARK 620 3 GLU B 105 OE1 93.3 58.5 REMARK 620 4 HIS D 36 ND1 101.5 88.9 147.3 REMARK 620 5 GLU D 105 OE2 95.5 136.1 97.3 110.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 106 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 53 ND1 REMARK 620 2 CYS B 92 SG 123.0 REMARK 620 3 HIS B 95 ND1 103.4 111.8 REMARK 620 4 LYS B 98 NZ 97.4 114.1 105.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 106 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 53 ND1 REMARK 620 2 CYS C 92 SG 124.2 REMARK 620 3 HIS C 95 ND1 102.9 116.2 REMARK 620 4 LYS C 98 NZ 97.7 113.3 98.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 106 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 53 ND1 REMARK 620 2 CYS D 92 SG 119.3 REMARK 620 3 HIS D 95 ND1 101.6 113.2 REMARK 620 4 LYS D 98 NZ 103.3 112.5 105.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 106 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AAC RELATED DB: PDB REMARK 900 NATIVE OXIDIZED AMICYANIN 1.3A STRUCTURE REMARK 900 RELATED ID: 2OV0 RELATED DB: PDB REMARK 900 HIGH RESOLUTION (0.75A) NATIVE OXIDIZED AMICYANIN STRUCTURE REMARK 900 RELATED ID: 3IE9 RELATED DB: PDB REMARK 900 STRUCTURE OF OXIDIZED M98L MUTANT OF AMICYANIN DBREF 3RYM A 1 105 UNP P22364 AMCY_PARDE 27 131 DBREF 3RYM B 1 105 UNP P22364 AMCY_PARDE 27 131 DBREF 3RYM C 1 105 UNP P22364 AMCY_PARDE 27 131 DBREF 3RYM D 1 105 UNP P22364 AMCY_PARDE 27 131 SEQADV 3RYM LYS A 98 UNP P22364 MET 124 ENGINEERED MUTATION SEQADV 3RYM LYS B 98 UNP P22364 MET 124 ENGINEERED MUTATION SEQADV 3RYM LYS C 98 UNP P22364 MET 124 ENGINEERED MUTATION SEQADV 3RYM LYS D 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 MET 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 LYS ARG GLY LYS VAL VAL VAL SEQRES 9 A 105 GLU SEQRES 1 B 105 ASP LYS ALA THR ILE PRO SER GLU SER PRO PHE ALA ALA SEQRES 2 B 105 ALA GLU VAL ALA ASP GLY ALA ILE VAL VAL ASP ILE ALA SEQRES 3 B 105 LYS MET LYS TYR GLU THR PRO GLU LEU HIS VAL LYS VAL SEQRES 4 B 105 GLY ASP THR VAL THR TRP ILE ASN ARG GLU ALA MET PRO SEQRES 5 B 105 HIS ASN VAL HIS PHE VAL ALA GLY VAL LEU GLY GLU ALA SEQRES 6 B 105 ALA LEU LYS GLY PRO MET MET LYS LYS GLU GLN ALA TYR SEQRES 7 B 105 SER LEU THR PHE THR GLU ALA GLY THR TYR ASP TYR HIS SEQRES 8 B 105 CYS THR PRO HIS PRO PHE LYS ARG GLY LYS VAL VAL VAL SEQRES 9 B 105 GLU SEQRES 1 C 105 ASP LYS ALA THR ILE PRO SER GLU SER PRO PHE ALA ALA SEQRES 2 C 105 ALA GLU VAL ALA ASP GLY ALA ILE VAL VAL ASP ILE ALA SEQRES 3 C 105 LYS MET LYS TYR GLU THR PRO GLU LEU HIS VAL LYS VAL SEQRES 4 C 105 GLY ASP THR VAL THR TRP ILE ASN ARG GLU ALA MET PRO SEQRES 5 C 105 HIS ASN VAL HIS PHE VAL ALA GLY VAL LEU GLY GLU ALA SEQRES 6 C 105 ALA LEU LYS GLY PRO MET MET LYS LYS GLU GLN ALA TYR SEQRES 7 C 105 SER LEU THR PHE THR GLU ALA GLY THR TYR ASP TYR HIS SEQRES 8 C 105 CYS THR PRO HIS PRO PHE LYS ARG GLY LYS VAL VAL VAL SEQRES 9 C 105 GLU SEQRES 1 D 105 ASP LYS ALA THR ILE PRO SER GLU SER PRO PHE ALA ALA SEQRES 2 D 105 ALA GLU VAL ALA ASP GLY ALA ILE VAL VAL ASP ILE ALA SEQRES 3 D 105 LYS MET LYS TYR GLU THR PRO GLU LEU HIS VAL LYS VAL SEQRES 4 D 105 GLY ASP THR VAL THR TRP ILE ASN ARG GLU ALA MET PRO SEQRES 5 D 105 HIS ASN VAL HIS PHE VAL ALA GLY VAL LEU GLY GLU ALA SEQRES 6 D 105 ALA LEU LYS GLY PRO MET MET LYS LYS GLU GLN ALA TYR SEQRES 7 D 105 SER LEU THR PHE THR GLU ALA GLY THR TYR ASP TYR HIS SEQRES 8 D 105 CYS THR PRO HIS PRO PHE LYS ARG GLY LYS VAL VAL VAL SEQRES 9 D 105 GLU HET ZN A 106 1 HET ZN A 107 1 HET ZN B 106 1 HET ZN B 107 1 HET ZN C 106 1 HET ZN D 106 1 HETNAM ZN ZINC ION FORMUL 5 ZN 6(ZN 2+) FORMUL 11 HOH *362(H2 O) HELIX 1 1 ALA A 14 VAL A 16 5 3 HELIX 2 2 ALA B 14 VAL B 16 5 3 HELIX 3 3 ALA C 14 VAL C 16 5 3 HELIX 4 4 ALA D 14 VAL D 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 4 ALA A 3 THR A 4 0 SHEET 2 B 4 GLN A 76 PHE A 82 -1 O THR A 81 N THR A 4 SHEET 3 B 4 THR A 42 ASN A 47 -1 N TRP A 45 O TYR A 78 SHEET 4 B 4 ILE A 21 ILE A 25 1 N ILE A 25 O ILE A 46 SHEET 1 C 3 GLU A 34 VAL A 37 0 SHEET 2 C 3 HIS A 95 VAL A 104 1 O VAL A 103 N LEU A 35 SHEET 3 C 3 GLY A 86 CYS A 92 -1 N GLY A 86 O VAL A 104 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 SHEET 1 E 3 ALA B 3 THR B 4 0 SHEET 2 E 3 GLN B 76 PHE B 82 -1 O THR B 81 N THR B 4 SHEET 3 E 3 PHE B 11 ALA B 12 -1 N PHE B 11 O ALA B 77 SHEET 1 F 4 ALA B 3 THR B 4 0 SHEET 2 F 4 GLN B 76 PHE B 82 -1 O THR B 81 N THR B 4 SHEET 3 F 4 THR B 42 ASN B 47 -1 N TRP B 45 O TYR B 78 SHEET 4 F 4 VAL B 22 ILE B 25 1 N ILE B 25 O ILE B 46 SHEET 1 G 3 GLU B 34 VAL B 37 0 SHEET 2 G 3 HIS B 95 VAL B 104 1 O VAL B 103 N LEU B 35 SHEET 3 G 3 GLY B 86 CYS B 92 -1 N GLY B 86 O VAL B 104 SHEET 1 H 2 HIS B 56 PHE B 57 0 SHEET 2 H 2 LEU B 67 LYS B 68 -1 O LEU B 67 N PHE B 57 SHEET 1 I 3 ALA C 3 THR C 4 0 SHEET 2 I 3 GLN C 76 PHE C 82 -1 O THR C 81 N THR C 4 SHEET 3 I 3 PHE C 11 ALA C 12 -1 N PHE C 11 O ALA C 77 SHEET 1 J 5 ALA C 3 THR C 4 0 SHEET 2 J 5 GLN C 76 PHE C 82 -1 O THR C 81 N THR C 4 SHEET 3 J 5 THR C 42 ASN C 47 -1 N TRP C 45 O TYR C 78 SHEET 4 J 5 VAL C 22 ALA C 26 1 N ILE C 25 O ILE C 46 SHEET 5 J 5 LYS C 29 TYR C 30 -1 O LYS C 29 N ALA C 26 SHEET 1 K 3 GLU C 34 VAL C 37 0 SHEET 2 K 3 ARG C 99 VAL C 104 1 O VAL C 103 N LEU C 35 SHEET 3 K 3 GLY C 86 HIS C 91 -1 N GLY C 86 O VAL C 104 SHEET 1 L 2 HIS C 56 PHE C 57 0 SHEET 2 L 2 LEU C 67 LYS C 68 -1 O LEU C 67 N PHE C 57 SHEET 1 M 3 ALA D 3 THR D 4 0 SHEET 2 M 3 GLN D 76 PHE D 82 -1 O THR D 81 N THR D 4 SHEET 3 M 3 PHE D 11 ALA D 12 -1 N PHE D 11 O ALA D 77 SHEET 1 N 4 ALA D 3 THR D 4 0 SHEET 2 N 4 GLN D 76 PHE D 82 -1 O THR D 81 N THR D 4 SHEET 3 N 4 THR D 42 ASN D 47 -1 N TRP D 45 O TYR D 78 SHEET 4 N 4 ILE D 21 ILE D 25 1 N ILE D 25 O ILE D 46 SHEET 1 O 3 GLU D 34 VAL D 37 0 SHEET 2 O 3 HIS D 95 VAL D 104 1 O VAL D 103 N LEU D 35 SHEET 3 O 3 GLY D 86 CYS D 92 -1 N GLY D 86 O VAL D 104 SHEET 1 P 2 HIS D 56 PHE D 57 0 SHEET 2 P 2 LEU D 67 LYS D 68 -1 O LEU D 67 N PHE D 57 LINK ND1 HIS A 36 ZN ZN A 107 1555 1555 2.06 LINK ND1 HIS A 53 ZN ZN A 106 1555 1555 2.06 LINK SG CYS A 92 ZN ZN A 106 1555 1555 2.33 LINK ND1 HIS A 95 ZN ZN A 106 1555 1555 2.13 LINK NZ LYS A 98 ZN ZN A 106 1555 1555 2.07 LINK OE2 GLU A 105 ZN ZN A 107 1555 1555 2.16 LINK OE1 GLU A 105 ZN ZN A 107 1555 1555 2.61 LINK ZN ZN A 107 ND1 HIS C 36 1555 1555 2.26 LINK ZN ZN A 107 OE2 GLU C 105 1555 1555 1.99 LINK ZN ZN A 107 OE1 GLU C 105 1555 1555 2.61 LINK ND1 HIS B 36 ZN ZN B 107 1555 1555 2.14 LINK ND1 HIS B 53 ZN ZN B 106 1555 1555 2.10 LINK SG CYS B 92 ZN ZN B 106 1555 1555 2.24 LINK ND1 HIS B 95 ZN ZN B 106 1555 1555 2.09 LINK NZ LYS B 98 ZN ZN B 106 1555 1555 2.27 LINK OE2 GLU B 105 ZN ZN B 107 1555 1555 1.94 LINK OE1 GLU B 105 ZN ZN B 107 1555 1555 2.45 LINK ZN ZN B 107 ND1 HIS D 36 1555 1555 2.14 LINK ZN ZN B 107 OE2 GLU D 105 1555 1555 2.18 LINK ND1 HIS C 53 ZN ZN C 106 1555 1555 2.05 LINK SG CYS C 92 ZN ZN C 106 1555 1555 2.28 LINK ND1 HIS C 95 ZN ZN C 106 1555 1555 2.09 LINK NZ LYS C 98 ZN ZN C 106 1555 1555 2.27 LINK ND1 HIS D 53 ZN ZN D 106 1555 1555 2.10 LINK SG CYS D 92 ZN ZN D 106 1555 1555 2.29 LINK ND1 HIS D 95 ZN ZN D 106 1555 1555 2.09 LINK NZ LYS D 98 ZN ZN D 106 1555 1555 2.15 SITE 1 AC1 4 HIS A 53 CYS A 92 HIS A 95 LYS A 98 SITE 1 AC2 4 HIS A 36 GLU A 105 HIS C 36 GLU C 105 SITE 1 AC3 4 HIS B 53 CYS B 92 HIS B 95 LYS B 98 SITE 1 AC4 4 HIS B 36 GLU B 105 HIS D 36 GLU D 105 SITE 1 AC5 4 HIS C 53 CYS C 92 HIS C 95 LYS C 98 SITE 1 AC6 4 HIS D 53 CYS D 92 HIS D 95 LYS D 98 CRYST1 37.367 51.668 56.543 105.97 96.48 108.35 P 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 0.026762 0.008878 0.006321 0.00000 SCALE2 0.000000 0.020392 0.007118 0.00000 SCALE3 0.000000 0.000000 0.018853 0.00000