10 20 30 40 50 60 70 80 1EP8 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSPORT 28-MAR-00 1EP8
TITLE CRYSTAL STRUCTURE OF A MUTATED THIOREDOXIN, D30A, FROM TITLE 2 CHLAMYDOMONAS REINHARDTII
COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN CH1, H-TYPE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHLAMYDOMONAS REINHARDTII; SOURCE 3 ORGANISM_TAXID: 3055; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS MUTANT, ELECTRON TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR V.MENCHISE,C.CORBIER,C.DIDIERJEAN,M.SAVIANO,E.BENEDETTI, AUTHOR 2 J.P.JACQUOT,A.AUBRY
REVDAT 3 24-FEB-09 1EP8 1 VERSN REVDAT 2 01-APR-03 1EP8 1 JRNL REVDAT 1 12-DEC-01 1EP8 0
JRNL AUTH V.MENCHISE,C.CORBIER,C.DIDIERJEAN,M.SAVIANO, JRNL AUTH 2 E.BENEDETTI,J.P.JACQUOT,A.AUBRY JRNL TITL CRYSTAL STRUCTURE OF THE WILD-TYPE AND D30A MUTANT JRNL TITL 2 THIOREDOXIN H OF CHLAMYDOMONAS REINHARDTII AND JRNL TITL 3 IMPLICATIONS FOR THE CATALYTIC MECHANISM. JRNL REF BIOCHEM.J. V. 359 65 2001 JRNL REFN ISSN 0264-6021 JRNL PMID 11563970 JRNL DOI 10.1042/0264-6021:3590065
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.MITTARD,M.J.BLACKLEDGE,M.STEIN,J.JACQUOT, REMARK 1 AUTH 2 D.MARION,J.M.LANCELIN REMARK 1 TITL NMR SOLUTION STRUCTURE OF AN OXIDIZED THIOREDOXIN REMARK 1 TITL 2 H FROM THE EUKARYOTIC GREEN ALGA CHLAMYDOMONAS REMARK 1 TITL 3 REINHARDTII REMARK 1 REF EUR.J.BIOCHEM. V. 243 374 1997 REMARK 1 REFN ISSN 0014-2956
REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10823 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1114 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL 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 : 1642 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 44 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) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 1.68 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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: THE TWO MOLECULES, A AND B, HAVE REMARK 3 BEEN REFINED INDEPENDENTLY, WITHOUT IMPOSING NON- REMARK 3 CRYSTALLOGRAPHIC 2-FOLD AXIS.
REMARK 4 REMARK 4 1EP8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-APR-00. REMARK 100 THE RCSB ID CODE IS RCSB010792.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-98 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 6.5 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 : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10823 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, PEG 10000, CACODYLATE, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 48.51700 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 97.03400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 97.03400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 48.51700 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 65 OD2 ASP B 65 1.84 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 SER A 3 44.01 140.95 REMARK 500 ALA A 97 43.08 -101.40 REMARK 500 ALA A 111 39.99 -70.53 REMARK 500 ALA B 111 46.96 -101.86 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EP7 RELATED DB: PDB REMARK 900 WT THIOREDOXIN
DBREF 1EP8 A 1 112 UNP P80028 TRXH_CHLRE 1 112 DBREF 1EP8 B 1 112 UNP P80028 TRXH_CHLRE 1 112
SEQADV 1EP8 ALA A 30 UNP P80028 ASP 30 ENGINEERED SEQADV 1EP8 ALA B 30 UNP P80028 ASP 30 ENGINEERED
SEQRES 1 A 112 GLY GLY SER VAL ILE VAL ILE ASP SER LYS ALA ALA TRP SEQRES 2 A 112 ASP ALA GLN LEU ALA LYS GLY LYS GLU GLU HIS LYS PRO SEQRES 3 A 112 ILE VAL VAL ALA PHE THR ALA THR TRP CYS GLY PRO CYS SEQRES 4 A 112 LYS MET ILE ALA PRO LEU PHE GLU THR LEU SER ASN ASP SEQRES 5 A 112 TYR ALA GLY LYS VAL ILE PHE LEU LYS VAL ASP VAL ASP SEQRES 6 A 112 ALA VAL ALA ALA VAL ALA GLU ALA ALA GLY ILE THR ALA SEQRES 7 A 112 MET PRO THR PHE HIS VAL TYR LYS ASP GLY VAL LYS ALA SEQRES 8 A 112 ASP ASP LEU VAL GLY ALA SER GLN ASP LYS LEU LYS ALA SEQRES 9 A 112 LEU VAL ALA LYS HIS ALA ALA ALA SEQRES 1 B 112 GLY GLY SER VAL ILE VAL ILE ASP SER LYS ALA ALA TRP SEQRES 2 B 112 ASP ALA GLN LEU ALA LYS GLY LYS GLU GLU HIS LYS PRO SEQRES 3 B 112 ILE VAL VAL ALA PHE THR ALA THR TRP CYS GLY PRO CYS SEQRES 4 B 112 LYS MET ILE ALA PRO LEU PHE GLU THR LEU SER ASN ASP SEQRES 5 B 112 TYR ALA GLY LYS VAL ILE PHE LEU LYS VAL ASP VAL ASP SEQRES 6 B 112 ALA VAL ALA ALA VAL ALA GLU ALA ALA GLY ILE THR ALA SEQRES 7 B 112 MET PRO THR PHE HIS VAL TYR LYS ASP GLY VAL LYS ALA SEQRES 8 B 112 ASP ASP LEU VAL GLY ALA SER GLN ASP LYS LEU LYS ALA SEQRES 9 B 112 LEU VAL ALA LYS HIS ALA ALA ALA
FORMUL 3 HOH *44(H2 O)
HELIX 1 1 SER A 9 HIS A 24 1 16 HELIX 2 2 CYS A 36 TYR A 53 1 18 HELIX 3 3 VAL A 67 ALA A 74 1 8 HELIX 4 4 SER A 98 ALA A 111 1 14 HELIX 5 5 SER B 9 HIS B 24 1 16 HELIX 6 6 CYS B 36 TYR B 53 1 18 HELIX 7 7 VAL B 67 GLY B 75 1 9 HELIX 8 8 SER B 98 ALA B 111 1 14
SHEET 1 A 5 ILE A 5 ILE A 7 0 SHEET 2 A 5 ILE A 58 ASP A 63 1 O PHE A 59 N ILE A 5 SHEET 3 A 5 ILE A 27 THR A 32 1 N VAL A 28 O ILE A 58 SHEET 4 A 5 THR A 81 LYS A 86 -1 O THR A 81 N PHE A 31 SHEET 5 A 5 VAL A 89 VAL A 95 -1 O VAL A 89 N LYS A 86 SHEET 1 B 5 ILE B 5 ILE B 7 0 SHEET 2 B 5 ILE B 58 ASP B 63 1 O PHE B 59 N ILE B 5 SHEET 3 B 5 ILE B 27 THR B 32 1 N VAL B 28 O ILE B 58 SHEET 4 B 5 THR B 81 LYS B 86 -1 O THR B 81 N PHE B 31 SHEET 5 B 5 VAL B 89 VAL B 95 -1 O VAL B 89 N LYS B 86
SSBOND 1 CYS A 36 CYS A 39 1555 1555 2.01 SSBOND 2 CYS B 36 CYS B 39 1555 1555 2.02
CISPEP 1 MET A 79 PRO A 80 0 0.05 CISPEP 2 MET B 79 PRO B 80 0 -0.70
CRYST1 49.692 49.692 145.551 90.00 90.00 120.00 P 31 2 1 12
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 0.020120 0.011620 0.000000 0.00000
SCALE2 0.000000 0.023240 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006870 0.00000