HEADER ELECTRON TRANSPORT 02-OCT-98 2RAC TITLE AMICYANIN REDUCED, PH 7.7, 1.3 ANGSTROMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (AMICYANIN); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARACOCCUS DENITRIFICANS; SOURCE 3 ORGANISM_TAXID: 266; SOURCE 4 STRAIN: NCIB 8944 KEYWDS ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR L.M.CUNANE,Z.-W.CHEN,R.C.E.DURLEY,F.S.MATHEWS REVDAT 7 30-AUG-23 2RAC 1 REMARK LINK REVDAT 6 04-OCT-17 2RAC 1 REMARK REVDAT 5 24-FEB-09 2RAC 1 VERSN REVDAT 4 01-APR-03 2RAC 1 JRNL REVDAT 3 16-JUN-00 2RAC 1 DBREF REVDAT 2 22-DEC-99 2RAC 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 07-OCT-98 2RAC 0 JRNL AUTH Z.ZHU,L.M.CUNANE,Z.CHEN,R.C.DURLEY,F.S.MATHEWS,V.L.DAVIDSON JRNL TITL MOLECULAR BASIS FOR INTERPROTEIN COMPLEX-DEPENDENT EFFECTS JRNL TITL 2 ON THE REDOX PROPERTIES OF AMICYANIN. JRNL REF BIOCHEMISTRY V. 37 17128 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9860825 JRNL DOI 10.1021/BI9817919 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.M.CUNANE,Z.-W.CHEN,R.C.E.DURLEY,F.S.MATHEWS REMARK 1 TITL X-RAY CRYSTAL STRUCTURE OF THE CUPREDOXIN AMICYANIN,FROM REMARK 1 TITL 2 PARACOCCUS DENITRIFICANS,REFINED AT 1.31 ANGSTROMS REMARK 1 TITL 3 RESOLUTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 52 676 1996 REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.7 REMARK 3 NUMBER OF REFLECTIONS : 18717 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1834 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.38 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2016 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 235 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 807 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 97 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.14 REMARK 3 ESD FROM SIGMAA (A) : 0.17 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.530 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.200 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.920 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.170 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.450 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : AMIRED7.PAR REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : AMIRED7.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RAC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008043. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 273.0 REMARK 200 PH : 7.70 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XUONG-HAMLIN MULTIWIRE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : UCSD-SYSTEM REMARK 200 DATA SCALING SOFTWARE : UCSD-SYSTEM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19838 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.16000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: 1AAC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.70 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 28.10000 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 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 VAL A 61 -60.98 -96.90 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 CU1 A 107 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 53 ND1 REMARK 620 2 CYS A 92 SG 154.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CU1 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: COPPER SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU1 A 107 REMARK 999 REMARK 999 SEQUENCE REMARK 999 IN SEQUENCE DATABASE 1-26 IS LEADER SEQUENCE DBREF 2RAC A 1 105 UNP P22364 AMCY_PARDE 27 131 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 MET ARG GLY LYS VAL VAL VAL SEQRES 9 A 105 GLU HET CU1 A 107 1 HETNAM CU1 COPPER (I) ION FORMUL 2 CU1 CU 1+ FORMUL 3 HOH *97(H2 O) HELIX 1 1 ALA A 13 GLU A 15 5 3 SHEET 1 A 3 ILE A 21 ILE A 25 0 SHEET 2 A 3 THR A 42 ASN A 47 1 N THR A 44 O ILE A 21 SHEET 3 A 3 ALA A 77 THR A 81 -1 N LEU A 80 O VAL A 43 SHEET 1 B 3 GLU A 34 VAL A 37 0 SHEET 2 B 3 ARG A 99 VAL A 104 1 N LYS A 101 O LEU A 35 SHEET 3 B 3 GLY A 86 HIS A 91 -1 N TYR A 90 O GLY A 100 LINK ND1 HIS A 53 CU CU1 A 107 1555 1555 1.90 LINK SG CYS A 92 CU CU1 A 107 1555 1555 2.12 SITE 1 CU1 5 CU1 A 107 HIS A 53 CYS A 92 HIS A 95 SITE 2 CU1 5 MET A 98 SITE 1 AC1 4 HIS A 53 CYS A 92 HIS A 95 MET A 98 CRYST1 28.750 56.200 27.420 90.00 96.12 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 0.034783 0.000000 0.003729 0.00000 SCALE2 0.000000 0.017793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036679 0.00000