HEADER OXIDOREDUCTASE 20-JUN-12 4FO5 TITLE CRYSTAL STRUCTURE OF A THIOREDOXIN-LIKE PROTEIN (BDI_1100) FROM TITLE 2 PARABACTEROIDES DISTASONIS ATCC 8503 AT 2.02 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARABACTEROIDES DISTASONIS; SOURCE 3 ORGANISM_TAXID: 435591; SOURCE 4 STRAIN: ATCC 8503; SOURCE 5 GENE: BDI_1100; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: PB1; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS AHPC/TSA FAMILY PROTEIN, STRUCTURAL GENOMICS, JOINT CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI- KEYWDS 3 BIOLOGY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 4 01-FEB-23 4FO5 1 REMARK SEQADV LINK REVDAT 3 24-JAN-18 4FO5 1 JRNL REVDAT 2 11-OCT-17 4FO5 1 REMARK REVDAT 1 04-JUL-12 4FO5 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF A THIOREDOXIN-LIKE PROTEIN (BDI_1100) JRNL TITL 2 FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 2.02 A JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK, REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 8027 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 + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.630 REMARK 3 FREE R VALUE TEST SET COUNT : 372 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 : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.26 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.75 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2269 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2060 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2165 REMARK 3 BIN R VALUE (WORKING SET) : 0.2041 REMARK 3 BIN FREE R VALUE : 0.2479 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.58 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 104 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 : 1043 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.60130 REMARK 3 B22 (A**2) : 2.77860 REMARK 3 B33 (A**2) : -9.37990 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.23220 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.305 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1080 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1468 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 508 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 29 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 162 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1080 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 148 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1281 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.99 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.95 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.86 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|25 - 165 } REMARK 3 ORIGIN FOR THE GROUP (A): 9.7594 24.0955 13.2980 REMARK 3 T TENSOR REMARK 3 T11: -0.1469 T22: -0.1395 REMARK 3 T33: -0.0511 T12: -0.0420 REMARK 3 T13: 0.0199 T23: -0.0230 REMARK 3 L TENSOR REMARK 3 L11: 6.0303 L22: 3.9827 REMARK 3 L33: 1.9246 L12: -0.7254 REMARK 3 L13: -0.3700 L23: -0.1490 REMARK 3 S TENSOR REMARK 3 S11: 0.0007 S12: 0.2467 S13: 0.0835 REMARK 3 S21: -0.1321 S22: 0.0218 S23: 0.0087 REMARK 3 S31: -0.0071 S32: -0.1158 S33: -0.0225 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1.A MET-INHIBITION PROTOCOL WAS USED REMARK 3 FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. REMARK 3 THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. 2.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B REMARK 3 FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U REMARK 3 FACTORS. 3.CHLORIDE (CL) MODELED IN THE SOLVENT STRUCTURE IS REMARK 3 PRESENT IN THE CRYSTALLIZATION CONDITION. 4.EXPERIMENTAL PHASES REMARK 3 FROM MAD PHASING WERE USED AS RESTRAINTS DURING CRYSTALLOGRAPHIC REMARK 3 REFINEMENT. REMARK 4 REMARK 4 4FO5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000073143. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91162,0.97922 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE DECEMBER 29, 2011 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8038 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 29.869 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM ACETATE, 30.0% REMARK 280 POLYETHYLENE GLYCOL 4000, 0.1M TRIS HYDROCHLORIDE PH 8.5, REMARK 280 NANODROP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.67150 REMARK 290 SMTRY3 2 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 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 A 0 REMARK 465 LEU A 42 REMARK 465 GLY A 43 REMARK 465 ASN A 44 REMARK 465 ASP A 45 REMARK 465 ALA A 46 REMARK 465 ILE A 166 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 LYS A 25 CG CD CE NZ REMARK 470 GLU A 40 CG CD OE1 OE2 REMARK 470 LYS A 47 CD CE NZ REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 GLU A 98 CG CD OE1 OE2 REMARK 470 LYS A 99 CE NZ REMARK 470 LYS A 108 CD CE NZ REMARK 470 GLU A 125 CG CD OE1 OE2 REMARK 470 GLU A 127 CG CD OE1 OE2 REMARK 470 LYS A 130 CG CD CE NZ REMARK 470 LYS A 131 CE NZ REMARK 470 GLU A 161 CG CD OE1 OE2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: JCSG-419068 RELATED DB: TARGETTRACK REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT (RESIDUES 25-166) WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 4FO5 A 25 166 UNP A6LAZ9 A6LAZ9_PARD8 25 166 SEQADV 4FO5 GLY A 0 UNP A6LAZ9 EXPRESSION TAG SEQRES 1 A 143 GLY LYS LEU THR GLU GLY VAL ASN PRO GLY ASP LEU ALA SEQRES 2 A 143 PRO ARG ILE GLU PHE LEU GLY ASN ASP ALA LYS ALA SER SEQRES 3 A 143 PHE HIS ASN GLN LEU GLY ARG TYR THR LEU LEU ASN PHE SEQRES 4 A 143 TRP ALA ALA TYR ASP ALA GLU SER ARG ALA ARG ASN VAL SEQRES 5 A 143 GLN LEU ALA ASN GLU VAL ASN LYS PHE GLY PRO ASP LYS SEQRES 6 A 143 ILE ALA MSE CYS SER ILE SER MSE ASP GLU LYS GLU SER SEQRES 7 A 143 ILE PHE THR GLU THR VAL LYS ILE ASP LYS LEU ASP LEU SEQRES 8 A 143 SER THR GLN PHE HIS GLU GLY LEU GLY LYS GLU SER GLU SEQRES 9 A 143 LEU TYR LYS LYS TYR ASP LEU ARG LYS GLY PHE LYS ASN SEQRES 10 A 143 PHE LEU ILE ASN ASP GLU GLY VAL ILE ILE ALA ALA ASN SEQRES 11 A 143 VAL THR PRO GLU LYS LEU THR GLU ILE LEU LYS ALA ILE MODRES 4FO5 MSE A 91 MET SELENOMETHIONINE MODRES 4FO5 MSE A 96 MET SELENOMETHIONINE HET MSE A 91 8 HET MSE A 96 8 HET CL A 200 1 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 CL CL 1- FORMUL 3 HOH *53(H2 O) HELIX 1 1 ASP A 67 ASN A 82 1 16 HELIX 2 2 LYS A 99 LYS A 111 1 13 HELIX 3 3 ASP A 113 SER A 115 5 3 HELIX 4 4 LEU A 122 GLU A 125 5 4 HELIX 5 5 SER A 126 TYR A 132 1 7 HELIX 6 6 ASP A 133 GLY A 137 5 5 HELIX 7 7 THR A 155 LYS A 164 1 10 SHEET 1 A 5 GLN A 117 HIS A 119 0 SHEET 2 A 5 ILE A 89 SER A 95 1 N SER A 93 O PHE A 118 SHEET 3 A 5 TYR A 57 TRP A 63 1 N ASN A 61 O ILE A 94 SHEET 4 A 5 ASN A 140 ILE A 143 -1 O ILE A 143 N THR A 58 SHEET 5 A 5 ILE A 149 ALA A 152 -1 O ILE A 150 N LEU A 142 LINK C ALA A 90 N MSE A 91 1555 1555 1.31 LINK C MSE A 91 N CYS A 92 1555 1555 1.31 LINK C SER A 95 N MSE A 96 1555 1555 1.34 LINK C MSE A 96 N ASP A 97 1555 1555 1.35 SITE 1 AC1 3 ARG A 38 ILE A 39 PHE A 50 CRYST1 33.164 49.343 40.523 90.00 112.18 90.00 P 1 21 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 0.030153 0.000000 0.012293 0.00000 SCALE2 0.000000 0.020266 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026649 0.00000