HEADER ELECTRON TRANSPORT 14-JUL-00 1FB0 TITLE CRYSTAL STRUCTURE OF THIOREDOXIN M FROM SPINACH CHLOROPLAST (REDUCED TITLE 2 FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN M; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: REDUCED FORM; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPINACIA OLERACEA; SOURCE 3 ORGANISM_COMMON: SPINACH; SOURCE 4 ORGANISM_TAXID: 3562; SOURCE 5 CELLULAR_LOCATION: CHLOROPLAST; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PKK233-2 (MODIFIED) KEYWDS ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR G.CAPITANI,Z.MARKOVIC-HOUSLEY,G.DELVAL,M.MORRIS,J.N.JANSONIUS, AUTHOR 2 P.SCHURMANN REVDAT 3 07-FEB-24 1FB0 1 REMARK REVDAT 2 24-FEB-09 1FB0 1 VERSN REVDAT 1 20-SEP-00 1FB0 0 JRNL AUTH G.CAPITANI,Z.MARKOVIC-HOUSLEY,G.DELVAL,M.MORRIS, JRNL AUTH 2 J.N.JANSONIUS,P.SCHURMANN JRNL TITL CRYSTAL STRUCTURES OF TWO FUNCTIONALLY DIFFERENT JRNL TITL 2 THIOREDOXINS IN SPINACH CHLOROPLASTS. JRNL REF J.MOL.BIOL. V. 302 135 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10964566 JRNL DOI 10.1006/JMBI.2000.4006 REMARK 2 REMARK 2 RESOLUTION. 2.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.40 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) (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 10890 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) : 0.198 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 593 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 : 1653 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.60 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) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 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: USED OVERALL ANISOTROPIC B-FACTOR REMARK 3 REFINEMENT AND BULK SOLVENT CORRECTION REMARK 3 (X-PLOR 3.851 AND CNS) REMARK 4 REMARK 4 1FB0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-00. REMARK 100 THE DEPOSITION ID IS D_1000011446. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-97 REMARK 200 TEMPERATURE (KELVIN) : 277 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 : ELLIOTT GX-20 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 : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10890 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.260 REMARK 200 RESOLUTION RANGE LOW (A) : 26.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.26900 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, PEG MONOMETHYLETHER REMARK 280 2000, AMMONIUM SULPHATE , PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 24.75333 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 49.50667 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 49.50667 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 24.75333 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A REMARK 300 MONOMER 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 400 REMARK 400 COMPOUND REMARK 400 ACTIVE SITE DISULPHIDE BRIDGE IS IN REDUCED FORM REMARK 400 (OBTAINED THROUGH A DTT SOAK). 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 B 8 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 9 114.73 70.20 REMARK 500 VAL B 21 -61.72 -94.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F9M RELATED DB: PDB REMARK 900 THIOREDOXIN F FROM SPINACH CHLOROPLAST (SHORT FORM) REMARK 900 RELATED ID: 1FAA RELATED DB: PDB REMARK 900 THIOREDOXIN F FROM SPINACH CHLOROPLAST (LONG FORM) REMARK 900 RELATED ID: 1FB6 RELATED DB: PDB REMARK 900 THIOREDOXIN M FROM SPINACH CHLOROPLAST (OXIDIZED FORM) DBREF 1FB0 A 8 112 UNP P07591 TRXM_SPIOL 75 179 DBREF 1FB0 B 8 112 UNP P07591 TRXM_SPIOL 75 179 SEQRES 1 A 105 GLU VAL GLN ASP VAL ASN ASP SER SER TRP LYS GLU PHE SEQRES 2 A 105 VAL LEU GLU SER GLU VAL PRO VAL MET VAL ASP PHE TRP SEQRES 3 A 105 ALA PRO TRP CYS GLY PRO CYS LYS LEU ILE ALA PRO VAL SEQRES 4 A 105 ILE ASP GLU LEU ALA LYS GLU TYR SER GLY LYS ILE ALA SEQRES 5 A 105 VAL TYR LYS LEU ASN THR ASP GLU ALA PRO GLY ILE ALA SEQRES 6 A 105 THR GLN TYR ASN ILE ARG SER ILE PRO THR VAL LEU PHE SEQRES 7 A 105 PHE LYS ASN GLY GLU ARG LYS GLU SER ILE ILE GLY ALA SEQRES 8 A 105 VAL PRO LYS SER THR LEU THR ASP SER ILE GLU LYS TYR SEQRES 9 A 105 LEU SEQRES 1 B 105 GLU VAL GLN ASP VAL ASN ASP SER SER TRP LYS GLU PHE SEQRES 2 B 105 VAL LEU GLU SER GLU VAL PRO VAL MET VAL ASP PHE TRP SEQRES 3 B 105 ALA PRO TRP CYS GLY PRO CYS LYS LEU ILE ALA PRO VAL SEQRES 4 B 105 ILE ASP GLU LEU ALA LYS GLU TYR SER GLY LYS ILE ALA SEQRES 5 B 105 VAL TYR LYS LEU ASN THR ASP GLU ALA PRO GLY ILE ALA SEQRES 6 B 105 THR GLN TYR ASN ILE ARG SER ILE PRO THR VAL LEU PHE SEQRES 7 B 105 PHE LYS ASN GLY GLU ARG LYS GLU SER ILE ILE GLY ALA SEQRES 8 B 105 VAL PRO LYS SER THR LEU THR ASP SER ILE GLU LYS TYR SEQRES 9 B 105 LEU FORMUL 3 HOH *113(H2 O) HELIX 1 1 SER A 16 VAL A 21 1 6 HELIX 2 2 CYS A 37 TYR A 54 1 18 HELIX 3 3 ALA A 68 TYR A 75 1 8 HELIX 4 4 PRO A 100 LEU A 112 1 13 HELIX 5 5 SER B 16 VAL B 21 1 6 HELIX 6 6 CYS B 37 TYR B 54 1 18 HELIX 7 7 ALA B 68 TYR B 75 1 8 HELIX 8 8 PRO B 100 TYR B 111 1 12 SHEET 1 A10 GLN A 10 ASP A 11 0 SHEET 2 A10 ALA A 59 ASN A 64 1 O VAL A 60 N GLN A 10 SHEET 3 A10 VAL A 28 TRP A 33 1 N MET A 29 O ALA A 59 SHEET 4 A10 THR A 82 LYS A 87 -1 O THR A 82 N PHE A 32 SHEET 5 A10 GLU A 90 GLY A 97 -1 O GLU A 90 N LYS A 87 SHEET 6 A10 GLU B 90 ILE B 96 1 O SER B 94 N ILE A 96 SHEET 7 A10 THR B 82 LYS B 87 -1 N VAL B 83 O ILE B 95 SHEET 8 A10 VAL B 28 TRP B 33 -1 N VAL B 28 O PHE B 86 SHEET 9 A10 ALA B 59 ASN B 64 1 O ALA B 59 N MET B 29 SHEET 10 A10 GLN B 10 ASP B 11 1 O GLN B 10 N LYS B 62 CISPEP 1 ILE A 80 PRO A 81 0 -0.28 CISPEP 2 ILE B 80 PRO B 81 0 -0.12 CRYST1 74.600 74.600 74.260 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 0.013405 0.007739 0.000000 0.00000 SCALE2 0.000000 0.015479 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013466 0.00000