HEADER ELECTRON TRANSPORT 27-JAN-98 1A3Z TITLE REDUCED RUSTICYANIN AT 1.9 ANGSTROMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUSTICYANIN; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: REDUCED FORM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACIDITHIOBACILLUS FERROOXIDANS; SOURCE 3 ORGANISM_TAXID: 920; SOURCE 4 CELLULAR_LOCATION: PERIPLASM KEYWDS CUPREDOXIN, METALLOPROTEIN, REDOX POTENTIAL, ACIDOPHILIC, ELECTRON KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR D.ZHAO,M.SHOHAM REVDAT 4 22-MAY-24 1A3Z 1 REMARK REVDAT 3 02-AUG-23 1A3Z 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1A3Z 1 VERSN REVDAT 1 29-JUL-98 1A3Z 0 JRNL AUTH D.ZHAO,M.SHOHAM JRNL TITL RUSTICYANIN: EXTREMES IN ACID STABILITY AND REDOX POTENTIAL JRNL TITL 2 EXPLAINED BY THE CRYSTAL STRUCTURE. JRNL REF BIOPHYS.J. V. 74 233 1998 JRNL REFN ISSN 0006-3495 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.L.WALTER,S.E.EALICK,A.M.FRIEDMAN,R.C.BLAKE II,P.PROCTOR, REMARK 1 AUTH 2 M.SHOHAM REMARK 1 TITL MULTIPLE WAVELENGTH ANOMALOUS DIFFRACTION (MAD) CRYSTAL REMARK 1 TITL 2 STRUCTURE OF RUSTICYANIN: A HIGHLY OXIDIZING CUPREDOXIN WITH REMARK 1 TITL 3 EXTREME ACID STABILITY REMARK 1 REF J.MOL.BIOL. V. 263 730 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.V.BOTUYAN,A.TOY-PALMER,J.CHUNG,R.C.BLAKE II,P.BEROZA, REMARK 1 AUTH 2 D.A.CASE,H.J.DYSON REMARK 1 TITL NMR SOLUTION STRUCTURE OF CU(I) RUSTICYANIN FROM REMARK 1 TITL 2 THIOBACILLUS FERROOXIDANS: STRUCTURAL BASIS FOR THE EXTREME REMARK 1 TITL 3 ACID STABILITY AND REDOX POTENTIAL REMARK 1 REF J.MOL.BIOL. V. 263 752 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.DJEBLI,P.PROCTOR,R.C.BLAKE II,M.SHOHAM REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC REMARK 1 TITL 2 STUDIES OF RUSTICYANIN FROM THIOBACILLUS FERROOXIDANS REMARK 1 REF J.MOL.BIOL. V. 227 581 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.4 REMARK 3 NUMBER OF REFLECTIONS : 9664 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) : 0.213 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 518 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 990 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE : 0.3680 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 52 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1133 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 85 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.00 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 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) : 3.042 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.984 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 4.240 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.579 ; NULL 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19.PEP REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170363. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUN-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4.6 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : ADSC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9718 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.4 REMARK 200 DATA REDUNDANCY : 1.970 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : 0.06300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.42 REMARK 200 R MERGE FOR SHELL (I) : 0.19900 REMARK 200 R SYM FOR SHELL (I) : 0.19900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.020 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: PHASES TAKEN FROM THE REMARK 200 OXIDIZED FORM, PDB ENTRY 1RCY REMARK 200 SOFTWARE USED: X-PLOR 3.8 REMARK 200 STARTING MODEL: PDB ENTRY 1RCY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION IN HANGING DROPS REMARK 280 AGAINST 100 MM-SODIUM CITRATE, PH 4.6, 200 MM LITHIUM CHLORIDE REMARK 280 AND 25%(W/V) PEG 8000 AT 277K. CRYSTALS SOAKED IN 10MM REMARK 280 DITHIONITE FOR 3 DAYS PRIOR TO DATA COLLECTION., VAPOR DIFFUSION REMARK 280 - HANGING DROP, VAPOR DIFFUSION, HANGING DROP 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 30.29500 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 THR A 2 REMARK 465 LEU A 3 REMARK 465 ASP A 4 REMARK 465 SER A 5 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 36 CG CD CE NZ 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 ASP A 29 44.01 -93.79 REMARK 500 VAL A 45 79.04 54.42 REMARK 500 ASN A 61 55.24 34.61 REMARK 500 PRO A 141 125.00 -38.99 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 156 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 85 ND1 REMARK 620 2 CYS A 138 SG 126.7 REMARK 620 3 HIS A 143 ND1 103.6 118.7 REMARK 620 4 MET A 148 SD 91.1 106.2 105.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CU REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: COPPER BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU1 A 156 DBREF 1A3Z A 1 155 UNP P24930 RUS2_THIFE 33 187 SEQADV 1A3Z ASP A 23 UNP P24930 THR 55 CONFLICT SEQADV 1A3Z VAL A 153 UNP P24930 ILE 185 CONFLICT SEQRES 1 A 155 GLY THR LEU ASP SER THR TRP LYS GLU ALA THR LEU PRO SEQRES 2 A 155 GLN VAL LYS ALA MET LEU GLU LYS ASP ASP GLY LYS VAL SEQRES 3 A 155 SER GLY ASP THR VAL THR TYR SER GLY LYS THR VAL HIS SEQRES 4 A 155 VAL VAL ALA ALA ALA VAL LEU PRO GLY PHE PRO PHE PRO SEQRES 5 A 155 SER PHE GLU VAL HIS ASP LYS LYS ASN PRO THR LEU GLU SEQRES 6 A 155 ILE PRO ALA GLY ALA THR VAL ASP VAL THR PHE ILE ASN SEQRES 7 A 155 THR ASN LYS GLY PHE GLY HIS SER PHE ASP ILE THR LYS SEQRES 8 A 155 LYS GLY PRO PRO TYR ALA VAL MET PRO VAL ILE ASP PRO SEQRES 9 A 155 ILE VAL ALA GLY THR GLY PHE SER PRO VAL PRO LYS ASP SEQRES 10 A 155 GLY LYS PHE GLY TYR THR ASP PHE THR TRP HIS PRO THR SEQRES 11 A 155 ALA GLY THR TYR TYR TYR VAL CYS GLN ILE PRO GLY HIS SEQRES 12 A 155 ALA ALA THR GLY MET PHE GLY LYS ILE VAL VAL LYS HET CU1 A 156 1 HETNAM CU1 COPPER (I) ION FORMUL 2 CU1 CU 1+ FORMUL 3 HOH *85(H2 O) HELIX 1 1 LEU A 12 LYS A 21 1 10 HELIX 2 2 ALA A 144 THR A 146 5 3 SHEET 1 A 5 LYS A 8 THR A 11 0 SHEET 2 A 5 LYS A 119 TRP A 127 -1 N TYR A 122 O LYS A 8 SHEET 3 A 5 THR A 71 ASN A 78 -1 N PHE A 76 O THR A 123 SHEET 4 A 5 THR A 37 ALA A 44 1 N VAL A 38 O THR A 71 SHEET 5 A 5 PHE A 54 VAL A 56 -1 N GLU A 55 O ALA A 43 SHEET 1 B 6 LYS A 25 SER A 27 0 SHEET 2 B 6 THR A 30 THR A 32 -1 N THR A 32 O LYS A 25 SHEET 3 B 6 THR A 63 ILE A 66 1 N THR A 63 O VAL A 31 SHEET 4 B 6 PHE A 149 VAL A 154 1 N VAL A 153 O LEU A 64 SHEET 5 B 6 GLY A 132 VAL A 137 -1 N TYR A 136 O GLY A 150 SHEET 6 B 6 ASP A 88 THR A 90 -1 N THR A 90 O TYR A 135 LINK ND1 HIS A 85 CU CU1 A 156 1555 1555 2.22 LINK SG CYS A 138 CU CU1 A 156 1555 1555 2.25 LINK ND1 HIS A 143 CU CU1 A 156 1555 1555 1.96 LINK SD MET A 148 CU CU1 A 156 1555 1555 2.75 CISPEP 1 PHE A 51 PRO A 52 0 -0.53 CISPEP 2 PRO A 94 PRO A 95 0 0.07 CISPEP 3 ASP A 103 PRO A 104 0 0.18 SITE 1 CU 5 HIS A 85 CYS A 138 HIS A 143 MET A 148 SITE 2 CU 5 CU1 A 156 SITE 1 AC1 4 HIS A 85 CYS A 138 HIS A 143 MET A 148 CRYST1 32.450 60.590 38.080 90.00 108.02 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 0.030817 0.000000 0.010025 0.00000 SCALE2 0.000000 0.016504 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027615 0.00000