PDB Short entry for 3WGE HEADER ISOMERASE 04-AUG-13 3WGE TITLE CRYSTAL STRUCTURE OF ERP46 TRX2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN DOMAIN-CONTAINING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TRX2 DOMAIN, UNP RESIDUES 190-298; COMPND 5 SYNONYM: ERP46, ENDOPLASMIC RETICULUM RESIDENT PROTEIN 46, ER PROTEIN COMPND 6 46, THIOREDOXIN-LIKE PROTEIN P46; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TXNDC5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C41(DE3)RIPL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: POPTG KEYWDS PDI FAMILY MEMBER, THIOREDOXIN DOMAIN, PROTEIN DISULFIDE ISOMERASE, KEYWDS 2 ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.INABA,M.SUZUKI,R.KOJIMA REVDAT 1 25-JUN-14 3WGE 0 JRNL AUTH R.KOJIMA,M.OKUMURA,S.MASUI,S.KANEMURA,M.INOUE,M.SAIKI, JRNL AUTH 2 H.YAMAGUCHI,T.HIKIMA,M.SUZUKI,S.AKIYAMA,K.INABA JRNL TITL RADICALLY DIFFERENT THIOREDOXIN DOMAIN ARRANGEMENT OF ERP46, JRNL TITL 2 AN EFFICIENT DISULFIDE BOND INTRODUCER OF THE MAMMALIAN PDI JRNL TITL 3 FAMILY JRNL REF STRUCTURE V. 22 431 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 24462249 JRNL DOI 10.1016/J.STR.2013.12.013 REMARK 2 REMARK 2 RESOLUTION. 0.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 70878 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.123 REMARK 3 R VALUE (WORKING SET) : 0.122 REMARK 3 FREE R VALUE : 0.135 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 3579 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 12.4767 - 2.8041 0.97 2723 149 0.1643 0.1471 REMARK 3 2 2.8041 - 2.2298 1.00 2697 125 0.1380 0.1471 REMARK 3 3 2.2298 - 1.9492 1.00 2632 148 0.1135 0.1302 REMARK 3 4 1.9492 - 1.7715 1.00 2633 142 0.1068 0.1143 REMARK 3 5 1.7715 - 1.6448 1.00 2612 132 0.1002 0.1241 REMARK 3 6 1.6448 - 1.5481 1.00 2620 130 0.0937 0.1200 REMARK 3 7 1.5481 - 1.4707 1.00 2600 156 0.0939 0.1124 REMARK 3 8 1.4707 - 1.4067 1.00 2550 163 0.0959 0.1140 REMARK 3 9 1.4067 - 1.3526 1.00 2598 135 0.0941 0.1256 REMARK 3 10 1.3526 - 1.3060 1.00 2567 134 0.0954 0.1190 REMARK 3 11 1.3060 - 1.2652 1.00 2599 125 0.0919 0.1080 REMARK 3 12 1.2652 - 1.2291 1.00 2598 129 0.0953 0.1209 REMARK 3 13 1.2291 - 1.1968 1.00 2603 120 0.0919 0.1024 REMARK 3 14 1.1968 - 1.1676 1.00 2567 126 0.0934 0.1260 REMARK 3 15 1.1676 - 1.1411 1.00 2579 156 0.0930 0.1191 REMARK 3 16 1.1411 - 1.1168 1.00 2539 134 0.0939 0.1156 REMARK 3 17 1.1168 - 1.0945 1.00 2581 137 0.0992 0.1068 REMARK 3 18 1.0945 - 1.0738 1.00 2548 146 0.1057 0.1376 REMARK 3 19 1.0738 - 1.0546 1.00 2521 163 0.1199 0.1457 REMARK 3 20 1.0546 - 1.0368 1.00 2583 135 0.1325 0.1385 REMARK 3 21 1.0368 - 1.0201 1.00 2561 124 0.1433 0.1525 REMARK 3 22 1.0201 - 1.0044 1.00 2554 135 0.1555 0.1669 REMARK 3 23 1.0044 - 0.9896 1.00 2572 125 0.1688 0.2085 REMARK 3 24 0.9896 - 0.9757 1.00 2540 151 0.1843 0.2031 REMARK 3 25 0.9757 - 0.9625 1.00 2550 128 0.1952 0.2168 REMARK 3 26 0.9625 - 0.9500 1.00 2572 131 0.2189 0.2399 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.83 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 : 0.012 1244 REMARK 3 ANGLE : 1.370 1712 REMARK 3 CHIRALITY : 0.083 163 REMARK 3 PLANARITY : 0.008 234 REMARK 3 DIHEDRAL : 12.779 489 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 3WGE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-AUG-13. REMARK 100 THE RCSB ID CODE IS RCSB096301. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7 REMARK 200 MONOCHROMATOR : DIP-6040 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70957 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 12.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL 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) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 <I/SIGMA(I)> 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 2.2M AMMONIUM SULFATE, PH REMARK 280 7.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 16.29000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.60000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.53000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.60000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.29000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.53000 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 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 THR A 297 REMARK 465 GLU A 298 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 HO2 GOL A 301 O HOH A 514 1.52 REMARK 500 O HOH A 507 O HOH A 528 2.10 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 HE ARG A 260 O HOH A 438 3755 1.59 REMARK 500 OE1 GLN A 229 O HOH A 513 4565 1.93 REMARK 500 NE2 GLN A 229 O HOH A 510 4565 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 217 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WGD RELATED DB: PDB DBREF 3WGE A 190 298 UNP Q8NBS9 TXND5_HUMAN 190 298 SEQADV 3WGE GLY A 186 UNP Q8NBS9 EXPRESSION TAG SEQADV 3WGE SER A 187 UNP Q8NBS9 EXPRESSION TAG SEQADV 3WGE HIS A 188 UNP Q8NBS9 EXPRESSION TAG SEQADV 3WGE MET A 189 UNP Q8NBS9 EXPRESSION TAG SEQRES 1 A 113 GLY SER HIS MET GLY LEU TYR GLU LEU SER ALA SER ASN SEQRES 2 A 113 PHE GLU LEU HIS VAL ALA GLN GLY ASP HIS PHE ILE LYS SEQRES 3 A 113 PHE PHE ALA PRO TRP CYS GLY HIS CYS LYS ALA LEU ALA SEQRES 4 A 113 PRO THR TRP GLU GLN LEU ALA LEU GLY LEU GLU HIS SER SEQRES 5 A 113 GLU THR VAL LYS ILE GLY LYS VAL ASP CYS THR GLN HIS SEQRES 6 A 113 TYR GLU LEU CYS SER GLY ASN GLN VAL ARG GLY TYR PRO SEQRES 7 A 113 THR LEU LEU TRP PHE ARG ASP GLY LYS LYS VAL ASP GLN SEQRES 8 A 113 TYR LYS GLY LYS ARG ASP LEU GLU SER LEU ARG GLU TYR SEQRES 9 A 113 VAL GLU SER GLN LEU GLN ARG THR GLU HET GOL A 301 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *137(H2 O) HELIX 1 1 ASN A 198 ALA A 204 1 7 HELIX 2 2 CYS A 217 LEU A 234 1 18 HELIX 3 3 HIS A 250 GLY A 256 1 7 HELIX 4 4 ASP A 282 GLN A 293 1 12 SHEET 1 A 5 LEU A 191 GLU A 193 0 SHEET 2 A 5 VAL A 240 ASP A 246 1 O ILE A 242 N TYR A 192 SHEET 3 A 5 ASP A 207 PHE A 213 1 N PHE A 213 O VAL A 245 SHEET 4 A 5 THR A 264 ARG A 269 -1 O THR A 264 N PHE A 212 SHEET 5 A 5 LYS A 272 TYR A 277 -1 O VAL A 274 N TRP A 267 SSBOND 1 CYS A 217 CYS A 220 1555 1555 2.28 SSBOND 2 CYS A 247 CYS A 254 1555 1555 2.04 CISPEP 1 TYR A 262 PRO A 263 0 -14.07 SITE 1 AC1 9 LEU A 191 TYR A 192 GLU A 193 GLN A 229 SITE 2 AC1 9 GLY A 233 ARG A 287 HOH A 442 HOH A 513 SITE 3 AC1 9 HOH A 514 CRYST1 32.580 39.060 87.200 90.00 90.00 90.00 P 21 21 21 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 0.030694 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025602 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011468 0.00000