HEADER ELECTRON TRANSPORT 15-JUL-99 1C09 TITLE RUBREDOXIN V44A CP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBREDOXIN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: RD; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PASTEURIANUM; SOURCE 3 ORGANISM_TAXID: 1501 KEYWDS IRON, METAL-BINDING, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR T.MIN,B.BEARD,C.KANG REVDAT 5 27-DEC-23 1C09 1 REMARK REVDAT 4 03-NOV-21 1C09 1 REMARK SEQADV REVDAT 3 24-FEB-09 1C09 1 VERSN REVDAT 2 01-APR-03 1C09 1 JRNL REVDAT 1 21-FEB-01 1C09 0 JRNL AUTH M.K.EIDSNESS,A.E.BURDEN,K.A.RICHIE,D.M.KURTZ JR.,R.A.SCOTT, JRNL AUTH 2 E.T.SMITH,T.ICHIYE,B.BEARD,T.MIN,C.KANG JRNL TITL MODULATION OF THE REDOX POTENTIAL OF THE [FE(SCYS)(4)] SITE JRNL TITL 2 IN RUBREDOXIN BY THE ORIENTATION OF A PEPTIDE DIPOLE. JRNL REF BIOCHEMISTRY V. 38 14803 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10555962 JRNL DOI 10.1021/BI991661F REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 17730 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1230 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 158 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) : 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 2.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.780 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1C09 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000001233. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 281 REMARK 200 PH : 4.5 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 : NI FILTER 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 : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.41700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA ACETATE PH 4.5, 2M AMMONIUM REMARK 280 SULFATE, TEMPERATURE 281K 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 28.71000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 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 GLU A 54 REMARK 465 GLU B 54 REMARK 465 GLU C 54 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 TRP A 37 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TRP A 37 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 TRP B 37 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TRP B 37 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 TRP C 37 CD1 - CG - CD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 TRP C 37 CE2 - CD2 - CG ANGL. DEV. = -5.6 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 ASP A 35 0.99 -67.67 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 116.5 REMARK 620 3 CYS A 39 SG 109.0 101.6 REMARK 620 4 CYS A 42 SG 102.7 112.8 114.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 55 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 6 SG REMARK 620 2 CYS B 9 SG 114.7 REMARK 620 3 CYS B 39 SG 112.3 100.4 REMARK 620 4 CYS B 42 SG 102.9 115.2 111.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE C 55 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 6 SG REMARK 620 2 CYS C 9 SG 115.9 REMARK 620 3 CYS C 39 SG 110.3 103.7 REMARK 620 4 CYS C 42 SG 101.8 112.3 113.2 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 FE A 55 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 55 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE C 55 DBREF 1C09 A 1 54 UNP P00268 RUBR_CLOPA 1 54 DBREF 1C09 B 1 54 UNP P00268 RUBR_CLOPA 1 54 DBREF 1C09 C 1 54 UNP P00268 RUBR_CLOPA 1 54 SEQADV 1C09 ALA A 44 UNP P00268 VAL 44 ENGINEERED MUTATION SEQADV 1C09 ALA B 44 UNP P00268 VAL 44 ENGINEERED MUTATION SEQADV 1C09 ALA C 44 UNP P00268 VAL 44 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 CYS GLY ALA GLY LYS ASP GLN PHE GLU GLU VAL SEQRES 5 A 54 GLU GLU SEQRES 1 B 54 MET LYS LYS TYR THR CYS THR VAL CYS GLY TYR ILE TYR SEQRES 2 B 54 ASN PRO GLU ASP GLY ASP PRO ASP ASN GLY VAL ASN PRO SEQRES 3 B 54 GLY THR ASP PHE LYS ASP ILE PRO ASP ASP TRP VAL CYS SEQRES 4 B 54 PRO LEU CYS GLY ALA GLY LYS ASP GLN PHE GLU GLU VAL SEQRES 5 B 54 GLU GLU SEQRES 1 C 54 MET LYS LYS TYR THR CYS THR VAL CYS GLY TYR ILE TYR SEQRES 2 C 54 ASN PRO GLU ASP GLY ASP PRO ASP ASN GLY VAL ASN PRO SEQRES 3 C 54 GLY THR ASP PHE LYS ASP ILE PRO ASP ASP TRP VAL CYS SEQRES 4 C 54 PRO LEU CYS GLY ALA GLY LYS ASP GLN PHE GLU GLU VAL SEQRES 5 C 54 GLU GLU HET FE A 55 1 HET FE B 55 1 HET FE C 55 1 HETNAM FE FE (III) ION FORMUL 4 FE 3(FE 3+) FORMUL 7 HOH *158(H2 O) HELIX 1 1 PRO A 20 GLY A 23 5 4 HELIX 2 2 ASP A 29 ILE A 33 5 5 HELIX 3 3 PRO B 20 GLY B 23 5 4 HELIX 4 4 ASP B 29 ILE B 33 5 5 HELIX 5 5 PRO C 20 GLY C 23 5 4 HELIX 6 6 ASP C 29 ILE C 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 SHEET 1 B 3 ILE B 12 TYR B 13 0 SHEET 2 B 3 TYR B 4 CYS B 6 -1 O TYR B 4 N TYR B 13 SHEET 3 B 3 PHE B 49 GLU B 51 -1 O GLU B 50 N THR B 5 SHEET 1 C 3 ILE C 12 TYR C 13 0 SHEET 2 C 3 TYR C 4 CYS C 6 -1 O TYR C 4 N TYR C 13 SHEET 3 C 3 PHE C 49 GLU C 51 -1 O GLU C 50 N THR C 5 LINK SG CYS A 6 FE FE A 55 1555 1555 2.32 LINK SG CYS A 9 FE FE A 55 1555 1555 2.32 LINK SG CYS A 39 FE FE A 55 1555 1555 2.32 LINK SG CYS A 42 FE FE A 55 1555 1555 2.30 LINK SG CYS B 6 FE FE B 55 1555 1555 2.31 LINK SG CYS B 9 FE FE B 55 1555 1555 2.30 LINK SG CYS B 39 FE FE B 55 1555 1555 2.31 LINK SG CYS B 42 FE FE B 55 1555 1555 2.30 LINK SG CYS C 6 FE FE C 55 1555 1555 2.32 LINK SG CYS C 9 FE FE C 55 1555 1555 2.31 LINK SG CYS C 39 FE FE C 55 1555 1555 2.32 LINK SG CYS C 42 FE FE C 55 1555 1555 2.31 SITE 1 AC1 4 CYS A 6 CYS A 9 CYS A 39 CYS A 42 SITE 1 AC2 4 CYS B 6 CYS B 9 CYS B 39 CYS B 42 SITE 1 AC3 4 CYS C 6 CYS C 9 CYS C 39 CYS C 42 CRYST1 38.348 57.420 38.503 90.00 112.74 90.00 P 1 21 1 6 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 0.026077 0.000000 0.010927 0.00000 SCALE2 0.000000 0.017416 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028160 0.00000