HEADER ELECTRON TRANSPORT 19-MAR-14 4P5S TITLE STRUCTURE OF REDUCED W45Y MUTANT OF AMICYANIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMICYANIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 27-131; COMPND 5 ENGINEERED: YES; COMPND 6 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS TYPE-I BLUE COPPER PROTEIN, BETA SANDWICH, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR N.SUKUMAR,V.L.DAVIDSON REVDAT 5 27-SEP-23 4P5S 1 REMARK REVDAT 4 25-DEC-19 4P5S 1 REMARK REVDAT 3 13-SEP-17 4P5S 1 SOURCE JRNL REMARK HET REVDAT 3 2 1 HETNAM FORMUL REVDAT 2 01-OCT-14 4P5S 1 JRNL REVDAT 1 23-APR-14 4P5S 0 JRNL AUTH B.A.DOW,N.SUKUMAR,J.O.MATOS,M.CHOI,A.SCHULTE,S.A.TATULIAN, JRNL AUTH 2 V.L.DAVIDSON JRNL TITL THE SOLE TRYPTOPHAN OF AMICYANIN ENHANCES ITS THERMAL JRNL TITL 2 STABILITY BUT DOES NOT INFLUENCE THE ELECTRONIC PROPERTIES JRNL TITL 3 OF THE TYPE 1 COPPER SITE. JRNL REF ARCH.BIOCHEM.BIOPHYS. V.-551 20 2014 JRNL REFN ESSN 1096-0384 JRNL PMID 24704124 JRNL DOI 10.1016/J.ABB.2014.03.010 REMARK 2 REMARK 2 RESOLUTION. 1.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.450 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 40205 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1985 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 28.3339 - 2.4563 0.96 2909 158 0.1588 0.1496 REMARK 3 2 2.4563 - 1.9498 0.94 2813 139 0.1552 0.1517 REMARK 3 3 1.9498 - 1.7034 0.97 2902 154 0.1451 0.1696 REMARK 3 4 1.7034 - 1.5477 0.93 2790 144 0.1279 0.1593 REMARK 3 5 1.5477 - 1.4367 0.95 2810 146 0.1224 0.1528 REMARK 3 6 1.4367 - 1.3520 0.94 2840 143 0.1158 0.1318 REMARK 3 7 1.3520 - 1.2843 0.93 2757 154 0.1166 0.1545 REMARK 3 8 1.2843 - 1.2284 0.93 2746 143 0.1094 0.1386 REMARK 3 9 1.2284 - 1.1811 0.93 2762 140 0.1032 0.1447 REMARK 3 10 1.1811 - 1.1404 0.93 2775 134 0.0986 0.1377 REMARK 3 11 1.1404 - 1.1047 0.92 2700 149 0.0936 0.1184 REMARK 3 12 1.1047 - 1.0731 0.90 2705 131 0.0968 0.1348 REMARK 3 13 1.0731 - 1.0449 0.89 2610 148 0.1055 0.1464 REMARK 3 14 1.0449 - 1.0200 0.70 2101 102 0.1251 0.1776 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.58 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 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 : 0.014 832 REMARK 3 ANGLE : 1.854 1132 REMARK 3 CHIRALITY : 0.106 127 REMARK 3 PLANARITY : 0.011 147 REMARK 3 DIHEDRAL : 10.630 305 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4P5S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000200723. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40243 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.020 REMARK 200 RESOLUTION RANGE LOW (A) : 28.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.13600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 11.80 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NATIVE AMICYANIN (1AAC) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: INITIAL CRYSTALS WERE OBTAINED FROM REMARK 280 HAMPTON RESEARCH AMMONIUM SULFATE SCREEN (HR2-211). BIGGER REMARK 280 CRYSTALS GROWN BY MACRO-SEEDING USING 3.2M NA/K PHOSPHATE REMARK 280 SOLUTION., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 28.32300 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLY A 19 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ALA A 20 CB REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 353 O HOH A 383 2849 2.13 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 ILE A 21 N - CA - CB ANGL. DEV. = -16.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 461 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 463 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A 464 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A 471 DISTANCE = 6.14 ANGSTROMS 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 CU1 A 201 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 53 ND1 REMARK 620 2 CYS A 92 SG 162.6 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU1 A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4P5R RELATED DB: PDB DBREF 4P5S A 1 105 UNP P22364 AMCY_PARDE 27 131 SEQADV 4P5S TYR A 45 UNP P22364 TRP 71 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 TYR 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 MET ARG GLY LYS VAL VAL VAL SEQRES 9 A 105 GLU HET CU1 A 201 1 HETNAM CU1 COPPER (I) ION FORMUL 2 CU1 CU 1+ FORMUL 3 HOH *171(H2 O) HELIX 1 AA1 ALA A 14 VAL A 16 5 3 SHEET 1 AA1 3 ALA A 3 THR A 4 0 SHEET 2 AA1 3 GLN A 76 PHE A 82 -1 O THR A 81 N THR A 4 SHEET 3 AA1 3 PHE A 11 ALA A 12 -1 N PHE A 11 O ALA A 77 SHEET 1 AA2 5 ALA A 3 THR A 4 0 SHEET 2 AA2 5 GLN A 76 PHE A 82 -1 O THR A 81 N THR A 4 SHEET 3 AA2 5 THR A 42 ASN A 47 -1 N VAL A 43 O LEU A 80 SHEET 4 AA2 5 ILE A 21 ALA A 26 1 N ILE A 21 O THR A 44 SHEET 5 AA2 5 LYS A 29 TYR A 30 -1 O LYS A 29 N ALA A 26 SHEET 1 AA3 3 GLU A 34 VAL A 37 0 SHEET 2 AA3 3 ARG A 99 VAL A 104 1 O VAL A 103 N LEU A 35 SHEET 3 AA3 3 GLY A 86 HIS A 91 -1 N GLY A 86 O VAL A 104 SHEET 1 AA4 2 HIS A 56 PHE A 57 0 SHEET 2 AA4 2 LEU A 67 LYS A 68 -1 O LEU A 67 N PHE A 57 LINK ND1 HIS A 53 CU CU1 A 201 1555 1555 1.91 LINK SG CYS A 92 CU CU1 A 201 1555 1555 2.11 SITE 1 AC1 4 HIS A 53 CYS A 92 HIS A 95 MET A 98 CRYST1 27.165 56.646 28.663 90.00 96.67 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 0.036812 0.000000 0.004304 0.00000 SCALE2 0.000000 0.017653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035126 0.00000