PDB Short entry for 1BE7 HEADER ELECTRON TRANSPORT 20-MAY-98 1BE7 TITLE CLOSTRIDIUM PASTEURIANUM RUBREDOXIN C42S MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PASTEURIANUM; SOURCE 3 ORGANISM_TAXID: 1501; SOURCE 4 CELLULAR_LOCATION: CYTOPLASM; SOURCE 5 GENE: CLORUB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 9 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PKK223-3; SOURCE 12 EXPRESSION_SYSTEM_GENE: CLORUB KEYWDS ELECTRON TRANSPORT, METALLOPROTEIN, IRON SULFUR, ELECTRON TRANSFER EXPDTA X-RAY DIFFRACTION AUTHOR M.MAHER,J.M.GUSS,M.WILCE,A.G.WEDD REVDAT 4 02-AUG-23 1BE7 1 REMARK REVDAT 3 03-NOV-21 1BE7 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1BE7 1 VERSN REVDAT 1 23-SEP-98 1BE7 0 JRNL AUTH Z.XIAO,M.J.LAVERY,M.AYHAN,S.D.B.SCROFANI,M.C.J.WILCE, JRNL AUTH 2 J.M.GUSS,P.A.TREGLOAN,G.N.GEORGE,A.G.WEDD JRNL TITL THE RUBREDOXIN FROM CLOSTRIDIUM PASTEURIANUM: MUTATION OF JRNL TITL 2 THE IRON CYSTEINYL LIGANDS TO SERINE. CRYSTAL AND MOLECULAR JRNL TITL 3 STRUCTURES OF THE OXIDISED AND DITHIONITE-TREATED FORMS OF JRNL TITL 4 THE CYS42SER MUTANT JRNL REF J.AM.CHEM.SOC. V. 120 4135 1998 JRNL REFN ISSN 0002-7863 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 6050 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 0.050 REMARK 3 FREE R VALUE TEST SET COUNT : 275 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 422 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.08 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.011 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.024 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.029 ; 0.040 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.117 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.179 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.259 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.086 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; 15.000 REMARK 3 PLANAR (DEGREES) : 5.700 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 16.800; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 14.700; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.157 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.284 ; 5.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.874 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.108 ; 8.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BE7 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_1000171649. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUL-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 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 : NI FILTER 0.00015" REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6061 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 0.06800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.14100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5RXN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLISED FROM 50-60% REMARK 280 SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT REMARK 280 PH 4., PH 4.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.26000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.62532 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 10.85667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 32.26000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 18.62532 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 10.85667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 32.26000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 18.62532 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 10.85667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.25064 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 21.71333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 37.25064 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 21.71333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 37.25064 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 21.71333 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: TRIMERIC 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 BIOMT1 2 -0.500000 -0.866025 0.000000 64.52000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 32.26000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 55.87596 REMARK 350 BIOMT3 3 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 TYR A 13 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES 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 CYS A 9 -11.08 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 FE A 55 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 CYS A 9 SG 112.2 REMARK 620 3 CYS A 39 SG 110.1 103.8 REMARK 620 4 SER A 42 OG 109.3 112.9 108.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: FEB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: FE BINDING SITE. MUTATION HAS REPLACED CYS 42 REMARK 800 WITH SER. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 55 DBREF 1BE7 A 1 54 UNP P00268 RUBR_CLOPA 1 54 SEQADV 1BE7 SER A 42 UNP P00268 CYS 42 ENGINEERED MUTATION SEQRES 1 A 54 MET LYS LYS TYR THR CYS THR VAL CYS GLY TYR ILE TYR SEQRES 2 A 54 ASN PRO GLU ASP GLY ASP PRO ASP ASN GLY VAL ASN PRO SEQRES 3 A 54 GLY THR ASP PHE LYS ASP ILE PRO ASP ASP TRP VAL CYS SEQRES 4 A 54 PRO LEU SER GLY VAL GLY LYS ASP GLN PHE GLU GLU VAL SEQRES 5 A 54 GLU GLU HET FE A 55 1 HETNAM FE FE (III) ION FORMUL 2 FE FE 3+ FORMUL 3 HOH *36(H2 O) HELIX 1 1 PRO A 20 GLY A 23 5 4 HELIX 2 2 ASP A 29 ILE A 33 5 5 SHEET 1 A 3 ILE A 12 TYR A 13 0 SHEET 2 A 3 TYR A 4 CYS A 6 -1 O TYR A 4 N TYR A 13 SHEET 3 A 3 PHE A 49 GLU A 51 -1 O GLU A 50 N THR A 5 LINK SG CYS A 6 FE FE A 55 1555 1555 2.29 LINK SG CYS A 9 FE FE A 55 1555 1555 2.29 LINK SG CYS A 39 FE FE A 55 1555 1555 2.31 LINK OG SER A 42 FE FE A 55 1555 1555 1.94 SITE 1 FEB 5 FE A 55 CYS A 6 CYS A 9 CYS A 39 SITE 2 FEB 5 SER A 42 SITE 1 AC1 4 CYS A 6 CYS A 9 CYS A 39 SER A 42 CRYST1 64.520 64.520 32.570 90.00 90.00 120.00 H 3 9 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 0.015499 0.008948 0.000000 0.00000 SCALE2 0.000000 0.017897 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030703 0.00000