HEADER ELECTRON TRANSPORT 15-JUN-05 1ZZY TITLE CRYSTAL STRUCTURE OF THIOREDOXIN MUTANT L7V COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRX1, TRX; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: TRXA, FIPA, TSNC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JF521; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTK100 KEYWDS ALPHA/BETA, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.A.GAVIRA,R.PEREZ-JIMENEZ,B.IBARRA-MOLERO,J.M.SANCHEZ-RUIZ REVDAT 6 23-AUG-23 1ZZY 1 REMARK REVDAT 5 20-OCT-21 1ZZY 1 REMARK SEQADV REVDAT 4 11-OCT-17 1ZZY 1 REMARK REVDAT 3 24-FEB-09 1ZZY 1 VERSN REVDAT 2 27-DEC-05 1ZZY 1 REMARK REVDAT 1 19-JUL-05 1ZZY 0 JRNL AUTH J.A.GAVIRA,R.PEREZ-JIMENEZ,B.IBARRA-MOLERO,J.M.SANCHEZ-RUIZ JRNL TITL CRYSTAL STRUCTURE OF THIOREDOXIN MUTANT L7V JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.69 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) (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 5499 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) : 0.223 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 283 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.016 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.61 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 593 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE : 0.4420 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 33 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.077 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1614 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.20000 REMARK 3 B22 (A**2) : -4.83000 REMARK 3 B33 (A**2) : -6.36000 REMARK 3 B12 (A**2) : -2.50000 REMARK 3 B13 (A**2) : -2.15000 REMARK 3 B23 (A**2) : 1.02000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.38 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.60 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 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) : 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 : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 50.89 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 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: XTALVIEW AND MOLBROBITY WERE ALSO USED REMARK 3 FOR THE REFINEMENT. REMARK 4 REMARK 4 1ZZY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033320. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 3.8 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MONTEL OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT, SADABS, XPREP, PROTEUM REMARK 200 PLUS 2 REMARK 200 DATA SCALING SOFTWARE : SAINT, SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5671 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.7 REMARK 200 DATA REDUNDANCY : 1.460 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12360 REMARK 200 FOR THE DATA SET : 6.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.38 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37400 REMARK 200 FOR SHELL : 2.820 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: A:2TRX.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM ACNA PH 3.8, 25% (V/V) ETOH, 10 REMARK 280 MM AC2CU, COUNTER-DIFFUSION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 SER A 1 REMARK 465 ASP A 2 REMARK 465 SER B 1 REMARK 465 ASP B 2 DBREF 1ZZY A 1 108 UNP P00274 THIO_ECOLI 1 108 DBREF 1ZZY B 1 108 UNP P00274 THIO_ECOLI 1 108 SEQADV 1ZZY VAL A 7 UNP P00274 LEU 7 ENGINEERED MUTATION SEQADV 1ZZY VAL B 7 UNP P00274 LEU 7 ENGINEERED MUTATION SEQRES 1 A 108 SER ASP LYS ILE ILE HIS VAL THR ASP ASP SER PHE ASP SEQRES 2 A 108 THR ASP VAL LEU LYS ALA ASP GLY ALA ILE LEU VAL ASP SEQRES 3 A 108 PHE TRP ALA GLU TRP CYS GLY PRO CYS LYS MET ILE ALA SEQRES 4 A 108 PRO ILE LEU ASP GLU ILE ALA ASP GLU TYR GLN GLY LYS SEQRES 5 A 108 LEU THR VAL ALA LYS LEU ASN ILE ASP GLN ASN PRO GLY SEQRES 6 A 108 THR ALA PRO LYS TYR GLY ILE ARG GLY ILE PRO THR LEU SEQRES 7 A 108 LEU LEU PHE LYS ASN GLY GLU VAL ALA ALA THR LYS VAL SEQRES 8 A 108 GLY ALA LEU SER LYS GLY GLN LEU LYS GLU PHE LEU ASP SEQRES 9 A 108 ALA ASN LEU ALA SEQRES 1 B 108 SER ASP LYS ILE ILE HIS VAL THR ASP ASP SER PHE ASP SEQRES 2 B 108 THR ASP VAL LEU LYS ALA ASP GLY ALA ILE LEU VAL ASP SEQRES 3 B 108 PHE TRP ALA GLU TRP CYS GLY PRO CYS LYS MET ILE ALA SEQRES 4 B 108 PRO ILE LEU ASP GLU ILE ALA ASP GLU TYR GLN GLY LYS SEQRES 5 B 108 LEU THR VAL ALA LYS LEU ASN ILE ASP GLN ASN PRO GLY SEQRES 6 B 108 THR ALA PRO LYS TYR GLY ILE ARG GLY ILE PRO THR LEU SEQRES 7 B 108 LEU LEU PHE LYS ASN GLY GLU VAL ALA ALA THR LYS VAL SEQRES 8 B 108 GLY ALA LEU SER LYS GLY GLN LEU LYS GLU PHE LEU ASP SEQRES 9 B 108 ALA ASN LEU ALA FORMUL 3 HOH *35(H2 O) HELIX 1 1 SER A 11 VAL A 16 1 6 HELIX 2 2 CYS A 32 TYR A 49 1 18 HELIX 3 3 GLY A 65 TYR A 70 1 6 HELIX 4 4 SER A 95 ALA A 108 1 14 HELIX 5 5 SER B 11 VAL B 16 1 6 HELIX 6 6 CYS B 32 TYR B 49 1 18 HELIX 7 7 GLY B 65 TYR B 70 1 6 HELIX 8 8 SER B 95 ALA B 108 1 14 SHEET 1 A 5 ILE A 5 HIS A 6 0 SHEET 2 A 5 THR A 54 ASN A 59 1 O LYS A 57 N ILE A 5 SHEET 3 A 5 ALA A 22 TRP A 28 1 N ASP A 26 O LEU A 58 SHEET 4 A 5 THR A 77 LYS A 82 -1 O LEU A 79 N VAL A 25 SHEET 5 A 5 GLU A 85 VAL A 91 -1 O ALA A 87 N LEU A 80 SHEET 1 B 5 ILE B 5 HIS B 6 0 SHEET 2 B 5 THR B 54 ASN B 59 1 O LYS B 57 N ILE B 5 SHEET 3 B 5 ALA B 22 TRP B 28 1 N ASP B 26 O LEU B 58 SHEET 4 B 5 THR B 77 LYS B 82 -1 O LEU B 79 N VAL B 25 SHEET 5 B 5 GLU B 85 VAL B 91 -1 O ALA B 87 N LEU B 80 SSBOND 1 CYS A 32 CYS A 35 1555 1555 2.02 SSBOND 2 CYS B 32 CYS B 35 1555 1555 2.02 CISPEP 1 ILE A 75 PRO A 76 0 0.02 CISPEP 2 ILE B 75 PRO B 76 0 0.06 CRYST1 33.658 36.597 42.836 78.43 67.38 88.39 P 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 0.029711 -0.000832 -0.012477 0.00000 SCALE2 0.000000 0.027335 -0.005744 0.00000 SCALE3 0.000000 0.000000 0.025844 0.00000