HEADER ELECTRON TRANSPORT 28-JUL-08 3DYR TITLE CRYSTAL STRUCTURE OF E. COLI THIOREDOXIN MUTANT I76T IN ITS OXIDIZED TITLE 2 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRX-1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: TRXA, FIPA, TSNC, B3781, JW5856; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MUTANT PROTEIN, ELECTRON TRANSPORT, HOST-VIRUS INTERACTION, REDOX- KEYWDS 2 ACTIVE CENTER, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR G.REN,J.C.A.BARDWELL,Z.XU REVDAT 6 09-OCT-24 3DYR 1 REMARK REVDAT 5 20-OCT-21 3DYR 1 REMARK SEQADV REVDAT 4 24-JUL-19 3DYR 1 REMARK REVDAT 3 25-OCT-17 3DYR 1 REMARK REVDAT 2 12-JAN-11 3DYR 1 JRNL REVDAT 1 27-JAN-09 3DYR 0 JRNL AUTH G.REN,D.STEPHAN,Z.XU,Y.ZHENG,D.TANG,R.S.HARRISON,M.KURZ, JRNL AUTH 2 R.JARROTT,S.R.SHOULDICE,A.HINIKER,J.L.MARTIN,B.HERAS, JRNL AUTH 3 J.C.BARDWELL JRNL TITL PROPERTIES OF THE THIOREDOXIN FOLD SUPERFAMILY ARE MODULATED JRNL TITL 2 BY A SINGLE AMINO ACID RESIDUE. JRNL REF J.BIOL.CHEM. V. 284 10150 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19181668 JRNL DOI 10.1074/JBC.M809509200 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 13345 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1071 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 25.6510 - 3.9930 0.98 1653 152 0.2490 0.2430 REMARK 3 2 3.9930 - 3.1710 0.98 1626 122 0.2290 0.2410 REMARK 3 3 3.1710 - 2.7710 0.97 1568 141 0.2620 0.2910 REMARK 3 4 2.7710 - 2.5180 0.94 1502 136 0.2620 0.3280 REMARK 3 5 2.5180 - 2.3370 0.94 1528 138 0.2420 0.3310 REMARK 3 6 2.3370 - 2.2000 0.93 1498 128 0.2390 0.3270 REMARK 3 7 2.2000 - 2.0890 0.91 1470 125 0.2410 0.3460 REMARK 3 8 2.0890 - 2.0000 0.88 1429 129 0.2590 0.3480 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 63.46 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.37800 REMARK 3 B22 (A**2) : -1.49100 REMARK 3 B33 (A**2) : 4.86900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.17200 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1632 REMARK 3 ANGLE : 1.038 2222 REMARK 3 CHIRALITY : 0.064 265 REMARK 3 PLANARITY : 0.005 286 REMARK 3 DIHEDRAL : 17.898 564 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3DYR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048657. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-08 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL 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 : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13739 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.24900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 29.39500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.69500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.39500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.69500 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY B 1 REMARK 465 SER B 2 REMARK 465 ALA B 110 REMARK 465 ALA B 111 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 21 CG OD1 OD2 REMARK 470 LYS A 53 CG CD CE NZ REMARK 470 LYS A 97 CG CD CE NZ REMARK 470 LYS A 101 CG CD CE NZ REMARK 470 GLU A 102 CG CD OE1 OE2 REMARK 470 ASP B 3 CG OD1 OD2 REMARK 470 HIS B 7 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 19 CG CD CE NZ REMARK 470 ASP B 21 CG OD1 OD2 REMARK 470 GLN B 51 CG CD OE1 NE2 REMARK 470 LYS B 53 CG CD CE NZ REMARK 470 LYS B 70 CG CD CE NZ REMARK 470 LYS B 83 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ILE A 73 CD1 REMARK 480 ILE B 61 CD1 REMARK 480 ILE B 73 CD1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 174 O HOH A 183 1565 2.12 REMARK 500 REMARK 500 REMARK: NULL DBREF 3DYR A 2 109 UNP P0AA25 THIO_ECOLI 2 109 DBREF 3DYR B 2 109 UNP P0AA25 THIO_ECOLI 2 109 SEQADV 3DYR GLY A 1 UNP P0AA25 EXPRESSION TAG SEQADV 3DYR THR A 76 UNP P0AA25 ILE 76 ENGINEERED MUTATION SEQADV 3DYR ALA A 110 UNP P0AA25 EXPRESSION TAG SEQADV 3DYR ALA A 111 UNP P0AA25 EXPRESSION TAG SEQADV 3DYR GLY B 1 UNP P0AA25 EXPRESSION TAG SEQADV 3DYR THR B 76 UNP P0AA25 ILE 76 ENGINEERED MUTATION SEQADV 3DYR ALA B 110 UNP P0AA25 EXPRESSION TAG SEQADV 3DYR ALA B 111 UNP P0AA25 EXPRESSION TAG SEQRES 1 A 111 GLY SER ASP LYS ILE ILE HIS LEU THR ASP ASP SER PHE SEQRES 2 A 111 ASP THR ASP VAL LEU LYS ALA ASP GLY ALA ILE LEU VAL SEQRES 3 A 111 ASP PHE TRP ALA GLU TRP CYS GLY PRO CYS LYS MET ILE SEQRES 4 A 111 ALA PRO ILE LEU ASP GLU ILE ALA ASP GLU TYR GLN GLY SEQRES 5 A 111 LYS LEU THR VAL ALA LYS LEU ASN ILE ASP GLN ASN PRO SEQRES 6 A 111 GLY THR ALA PRO LYS TYR GLY ILE ARG GLY THR PRO THR SEQRES 7 A 111 LEU LEU LEU PHE LYS ASN GLY GLU VAL ALA ALA THR LYS SEQRES 8 A 111 VAL GLY ALA LEU SER LYS GLY GLN LEU LYS GLU PHE LEU SEQRES 9 A 111 ASP ALA ASN LEU ALA ALA ALA SEQRES 1 B 111 GLY SER ASP LYS ILE ILE HIS LEU THR ASP ASP SER PHE SEQRES 2 B 111 ASP THR ASP VAL LEU LYS ALA ASP GLY ALA ILE LEU VAL SEQRES 3 B 111 ASP PHE TRP ALA GLU TRP CYS GLY PRO CYS LYS MET ILE SEQRES 4 B 111 ALA PRO ILE LEU ASP GLU ILE ALA ASP GLU TYR GLN GLY SEQRES 5 B 111 LYS LEU THR VAL ALA LYS LEU ASN ILE ASP GLN ASN PRO SEQRES 6 B 111 GLY THR ALA PRO LYS TYR GLY ILE ARG GLY THR PRO THR SEQRES 7 B 111 LEU LEU LEU PHE LYS ASN GLY GLU VAL ALA ALA THR LYS SEQRES 8 B 111 VAL GLY ALA LEU SER LYS GLY GLN LEU LYS GLU PHE LEU SEQRES 9 B 111 ASP ALA ASN LEU ALA ALA ALA FORMUL 3 HOH *135(H2 O) HELIX 1 1 SER A 12 VAL A 17 1 6 HELIX 2 2 CYS A 33 TYR A 50 1 18 HELIX 3 3 GLY A 66 TYR A 71 1 6 HELIX 4 4 SER A 96 ALA A 110 1 15 HELIX 5 5 SER B 12 VAL B 17 1 6 HELIX 6 6 CYS B 33 TYR B 50 1 18 HELIX 7 7 THR B 67 GLY B 72 5 6 HELIX 8 8 SER B 96 ALA B 109 1 14 SHEET 1 A 5 ILE A 6 LEU A 8 0 SHEET 2 A 5 THR A 55 ASN A 60 1 O LYS A 58 N ILE A 6 SHEET 3 A 5 ILE A 24 TRP A 29 1 N LEU A 25 O ALA A 57 SHEET 4 A 5 THR A 78 LYS A 83 -1 O PHE A 82 N ILE A 24 SHEET 5 A 5 GLU A 86 VAL A 92 -1 O ALA A 88 N LEU A 81 SHEET 1 B 5 ILE B 6 HIS B 7 0 SHEET 2 B 5 LEU B 54 ASN B 60 1 O VAL B 56 N ILE B 6 SHEET 3 B 5 ALA B 23 TRP B 29 1 N ASP B 27 O ALA B 57 SHEET 4 B 5 THR B 78 LYS B 83 -1 O THR B 78 N PHE B 28 SHEET 5 B 5 GLU B 86 VAL B 92 -1 O GLU B 86 N LYS B 83 SSBOND 1 CYS A 33 CYS A 36 1555 1555 2.03 SSBOND 2 CYS B 33 CYS B 36 1555 1555 2.04 CISPEP 1 THR A 76 PRO A 77 0 -0.95 CISPEP 2 THR B 76 PRO B 77 0 -4.49 CRYST1 58.790 39.390 90.550 90.00 96.63 90.00 C 1 2 1 8 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 0.017010 0.000000 0.001977 0.00000 SCALE2 0.000000 0.025387 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011118 0.00000