HEADER OXIDOREDUCTASE 02-NOV-12 4HU9 TITLE E. COLI THIOREDOXIN VARIANT WITH (4S)-FLUOROPRO76 AS SINGLE PROLINE TITLE 2 RESIDUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN-1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: TRXA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM83; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTRX1P KEYWDS 4S-FLUOROPROLINE, CISPROLINE, THIOREDOXIN FOLD, PROTEIN DISULFIDE KEYWDS 2 OXIDOREDUCTASE ACTIVITY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHARER,M.RUBINI,G.CAPITANI,R.GLOCKSHUBER REVDAT 3 20-SEP-17 4HU9 1 REMARK REVDAT 2 03-JUL-13 4HU9 1 JRNL REVDAT 1 29-MAY-13 4HU9 0 JRNL AUTH M.RUBINI,M.A.SCHARER,G.CAPITANI,R.GLOCKSHUBER JRNL TITL (4R)- AND (4S)-FLUOROPROLINE IN THE CONSERVED CIS-PROLYL JRNL TITL 2 PEPTIDE BOND OF THE THIOREDOXIN FOLD: TERTIARY STRUCTURE JRNL TITL 3 CONTEXT DICTATES RING PUCKERING. JRNL REF CHEMBIOCHEM V. 14 1053 2013 JRNL REFN ISSN 1439-4227 JRNL PMID 23712956 JRNL DOI 10.1002/CBIC.201300178 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 18987 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1007 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 43.1975 - 2.9652 1.00 2648 149 0.1540 0.1664 REMARK 3 2 2.9652 - 2.3536 0.99 2573 144 0.1675 0.2367 REMARK 3 3 2.3536 - 2.0561 1.00 2582 144 0.1516 0.1888 REMARK 3 4 2.0561 - 1.8681 1.00 2555 143 0.1569 0.2014 REMARK 3 5 1.8681 - 1.7342 1.00 2590 145 0.1775 0.2397 REMARK 3 6 1.7342 - 1.6320 1.00 2572 144 0.2133 0.2689 REMARK 3 7 1.6320 - 1.5502 0.95 2460 138 0.3036 0.3425 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.67 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 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 : 0.007 868 REMARK 3 ANGLE : 1.000 1181 REMARK 3 CHIRALITY : 0.069 140 REMARK 3 PLANARITY : 0.003 152 REMARK 3 DIHEDRAL : 12.164 308 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 4HU9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000075927. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR WITH DUAL REMARK 200 CHANNEL CUT CRYSTALS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19020 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 43.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.19200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM ACETIC ACID-NAOH, 2 MM CUCL2, 30 REMARK 280 % (V/V) MPD, PH 4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277.15K 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 44.13500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.38000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.13500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.38000 REMARK 290 SMTRY3 4 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: MONOMERIC 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 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 LYS A 52 CD CE NZ REMARK 480 ARG A 73 NE CZ NH1 NH2 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 O HOH A 349 O HOH A 438 2.09 REMARK 500 O HOH A 438 O HOH A 446 2.15 REMARK 500 O HOH A 375 O HOH A 417 2.15 REMARK 500 O HOH A 372 O HOH A 391 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 318 O HOH A 365 4455 2.17 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 CU A 201 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 2 N REMARK 620 2 SER A 1 N 85.4 REMARK 620 3 SER A 1 N 84.4 1.7 REMARK 620 4 ASP A 2 OD1 94.0 171.3 172.5 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 CU A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HU7 RELATED DB: PDB REMARK 900 RELATED ID: 4HUA RELATED DB: PDB DBREF 4HU9 A 1 108 UNP P0AA25 THIO_ECOLI 2 109 SEQADV 4HU9 ALA A 34 UNP P0AA25 PRO 35 ENGINEERED MUTATION SEQADV 4HU9 ALA A 40 UNP P0AA25 PRO 41 ENGINEERED MUTATION SEQADV 4HU9 ALA A 64 UNP P0AA25 PRO 65 ENGINEERED MUTATION SEQADV 4HU9 ALA A 68 UNP P0AA25 PRO 69 ENGINEERED MUTATION SEQRES 1 A 108 SER ASP LYS ILE ILE HIS LEU 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 ALA CYS LYS MET ILE ALA SEQRES 4 A 108 ALA 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 ALA GLY SEQRES 6 A 108 THR ALA ALA LYS TYR GLY ILE ARG GLY ILE 4FB 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 MODRES 4HU9 4FB A 76 PRO (4S)-4-FLUORO-L-PROLINE HET 4FB A 76 8 HET CU A 201 1 HETNAM 4FB (4S)-4-FLUORO-L-PROLINE HETNAM CU COPPER (II) ION FORMUL 1 4FB C5 H8 F N O2 FORMUL 2 CU CU 2+ FORMUL 3 HOH *159(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 ASN A 63 TYR A 70 1 8 HELIX 4 4 SER A 95 ALA A 105 1 11 SHEET 1 A 5 ILE A 4 LEU A 7 0 SHEET 2 A 5 THR A 54 ASN A 59 1 O LYS A 57 N LEU A 7 SHEET 3 A 5 ALA A 22 TRP A 28 1 N LEU A 24 O THR A 54 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 SSBOND 1 CYS A 32 CYS A 35 1555 1555 2.05 LINK C 4FB A 76 N THR A 77 1555 1555 1.33 LINK N ASP A 2 CU CU A 201 1555 1555 1.94 LINK N BSER A 1 CU CU A 201 1555 1555 1.97 LINK N ASER A 1 CU CU A 201 1555 1555 1.98 LINK OD1 ASP A 2 CU CU A 201 1555 1555 1.99 LINK C ILE A 75 N 4FB A 76 1555 1555 1.33 CISPEP 1 ILE A 75 4FB A 76 0 -1.91 SITE 1 AC1 5 SER A 1 ASP A 2 LYS A 3 ASP A 10 SITE 2 AC1 5 HOH A 315 CRYST1 88.270 48.760 31.570 90.00 101.94 90.00 C 1 2 1 4 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 0.011329 0.000000 0.002395 0.00000 SCALE2 0.000000 0.020509 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032376 0.00000