HEADER OXIDOREDUCTASE 24-AUG-15 5DCH TITLE CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA DSBA E82I IN COMPLEX WITH TITLE 2 MIPS-0000851 (3-[(2-METHYLBENZYL)SULFANYL]-4H-1,2,4-TRIAZOL-4-AMINE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228; SOURCE 5 GENE: DSBA, PA5489; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS THIOREDOXIN FOLD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.M.MCMAHON,J.L.MARTIN REVDAT 4 27-SEP-23 5DCH 1 REMARK REVDAT 3 01-JAN-20 5DCH 1 REMARK REVDAT 2 12-APR-17 5DCH 1 JRNL REVDAT 1 05-OCT-16 5DCH 0 JRNL AUTH B.MOHANTY,K.RIMMER,R.M.MCMAHON,S.J.HEADEY,M.VAZIRANI, JRNL AUTH 2 S.R.SHOULDICE,M.COINCON,S.TAY,C.J.MORTON,J.S.SIMPSON, JRNL AUTH 3 J.L.MARTIN,M.J.SCANLON JRNL TITL FRAGMENT LIBRARY SCREENING IDENTIFIES HITS THAT BIND TO THE JRNL TITL 2 NON-CATALYTIC SURFACE OF PSEUDOMONAS AERUGINOSA DSBA1. JRNL REF PLOS ONE V. 12 73436 2017 JRNL REFN ESSN 1932-6203 JRNL PMID 28346540 JRNL DOI 10.1371/JOURNAL.PONE.0173436 REMARK 2 REMARK 2 RESOLUTION. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 31303 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1574 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 35.1079 - 3.2175 0.98 2813 149 0.1563 0.1577 REMARK 3 2 3.2175 - 2.5541 0.97 2740 151 0.1404 0.1627 REMARK 3 3 2.5541 - 2.2313 0.97 2759 131 0.1172 0.1579 REMARK 3 4 2.2313 - 2.0273 0.97 2718 159 0.1114 0.1483 REMARK 3 5 2.0273 - 1.8820 0.97 2715 138 0.1122 0.1401 REMARK 3 6 1.8820 - 1.7710 0.97 2723 140 0.1133 0.1736 REMARK 3 7 1.7710 - 1.6823 0.95 2628 157 0.1205 0.1672 REMARK 3 8 1.6823 - 1.6091 0.96 2671 160 0.1258 0.1704 REMARK 3 9 1.6091 - 1.5472 0.95 2688 124 0.1380 0.1943 REMARK 3 10 1.5472 - 1.4938 0.95 2667 133 0.1669 0.2350 REMARK 3 11 1.4938 - 1.4471 0.93 2607 132 0.1948 0.2402 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.19 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 : 0.008 1620 REMARK 3 ANGLE : 1.148 2203 REMARK 3 CHIRALITY : 0.064 233 REMARK 3 PLANARITY : 0.006 278 REMARK 3 DIHEDRAL : 12.829 616 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 5DCH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212829. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95370 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31349 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.447 REMARK 200 RESOLUTION RANGE LOW (A) : 35.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 1.08100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: 3H93 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-29 % PEG 1500, 0.1 M MES, PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 31.55000 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 SER A 1 REMARK 465 ASN A 2 REMARK 465 ALA A 3 REMARK 465 ASP A 4 REMARK 465 LYS A 192 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 HG SER A 22 O HOH A 303 1.53 REMARK 500 HZ3 LYS A 140 O HOH A 301 1.60 REMARK 500 NZ LYS A 140 O HOH A 301 1.87 REMARK 500 OH TYR A 41 O HOH A 302 2.06 REMARK 500 O HOH A 342 O HOH A 388 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 10 -79.37 -106.27 REMARK 500 LEU A 66 74.30 -101.33 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 1YO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 206 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2MBU RELATED DB: PDB REMARK 900 2MBU CONTAINS THE SAME PROTEIN-LIGAND COMPLEX DETERMINED BY REMARK 900 SOLUTION NMR METHODS. REMARK 900 RELATED ID: 4ZL7 RELATED DB: PDB REMARK 900 RELATED ID: 4ZL8 RELATED DB: PDB REMARK 900 RELATED ID: 4ZL9 RELATED DB: PDB DBREF 5DCH A 3 192 UNP P0C2B2 DSBA_PSEAE 22 211 SEQADV 5DCH SER A 1 UNP P0C2B2 EXPRESSION TAG SEQADV 5DCH ASN A 2 UNP P0C2B2 EXPRESSION TAG SEQADV 5DCH ILE A 82 UNP P0C2B2 GLU 101 ENGINEERED MUTATION SEQRES 1 A 192 SER ASN ALA ASP ASP TYR THR ALA GLY LYS GLU TYR VAL SEQRES 2 A 192 GLU LEU SER SER PRO VAL PRO VAL SER GLN PRO GLY LYS SEQRES 3 A 192 ILE GLU VAL VAL GLU LEU PHE TRP TYR GLY CYS PRO HIS SEQRES 4 A 192 CYS TYR ALA PHE GLU PRO THR ILE VAL PRO TRP SER GLU SEQRES 5 A 192 LYS LEU PRO ALA ASP VAL HIS PHE VAL ARG LEU PRO ALA SEQRES 6 A 192 LEU PHE GLY GLY ILE TRP ASN VAL HIS GLY GLN MET PHE SEQRES 7 A 192 LEU THR LEU ILE SER MET GLY VAL GLU HIS ASP VAL HIS SEQRES 8 A 192 ASN ALA VAL PHE GLU ALA ILE HIS LYS GLU HIS LYS LYS SEQRES 9 A 192 LEU ALA THR PRO GLU GLU MET ALA ASP PHE LEU ALA GLY SEQRES 10 A 192 LYS GLY VAL ASP LYS GLU LYS PHE LEU SER THR TYR ASN SEQRES 11 A 192 SER PHE ALA ILE LYS GLY GLN MET GLU LYS ALA LYS LYS SEQRES 12 A 192 LEU ALA MET ALA TYR GLN VAL THR GLY VAL PRO THR MET SEQRES 13 A 192 VAL VAL ASN GLY LYS TYR ARG PHE ASP ILE GLY SER ALA SEQRES 14 A 192 GLY GLY PRO GLU GLU THR LEU LYS LEU ALA ASP TYR LEU SEQRES 15 A 192 ILE GLU LYS GLU ARG ALA ALA ALA LYS LYS HET 1YO A 201 15 HET GOL A 202 14 HET GOL A 203 14 HET GOL A 204 14 HET GOL A 205 14 HET MES A 206 25 HETNAM 1YO 3-[(2-METHYLBENZYL)SULFANYL]-4H-1,2,4-TRIAZOL-4-AMINE HETNAM GOL GLYCEROL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 1YO C10 H12 N4 S FORMUL 3 GOL 4(C3 H8 O3) FORMUL 7 MES C6 H13 N O4 S FORMUL 8 HOH *141(H2 O) HELIX 1 AA1 CYS A 37 LYS A 53 1 17 HELIX 2 AA2 GLY A 69 MET A 84 1 16 HELIX 3 AA3 VAL A 86 LYS A 100 1 15 HELIX 4 AA4 THR A 107 GLY A 117 1 11 HELIX 5 AA5 ASP A 121 ASN A 130 1 10 HELIX 6 AA6 SER A 131 GLN A 149 1 19 HELIX 7 AA7 ILE A 166 GLY A 170 1 5 HELIX 8 AA8 GLY A 171 ALA A 189 1 19 SHEET 1 AA1 5 VAL A 13 GLU A 14 0 SHEET 2 AA1 5 TYR A 162 ASP A 165 -1 O ARG A 163 N VAL A 13 SHEET 3 AA1 5 THR A 155 VAL A 158 -1 N MET A 156 O PHE A 164 SHEET 4 AA1 5 ILE A 27 PHE A 33 -1 N LEU A 32 O THR A 155 SHEET 5 AA1 5 VAL A 58 PRO A 64 1 O VAL A 61 N VAL A 29 SSBOND 1 CYS A 37 CYS A 40 1555 1555 2.03 CISPEP 1 VAL A 153 PRO A 154 0 -5.04 SITE 1 AC1 10 PRO A 20 SER A 22 GLU A 28 LEU A 79 SITE 2 AC1 10 GLN A 137 LYS A 140 LEU A 144 TYR A 148 SITE 3 AC1 10 HOH A 355 HOH A 382 SITE 1 AC2 8 CYS A 37 GLY A 152 VAL A 153 ARG A 187 SITE 2 AC2 8 GOL A 205 HOH A 333 HOH A 340 HOH A 409 SITE 1 AC3 8 LYS A 10 VAL A 13 GLY A 117 ARG A 163 SITE 2 AC3 8 PHE A 164 ASP A 165 HOH A 307 HOH A 329 SITE 1 AC4 1 ALA A 147 SITE 1 AC5 7 GLY A 25 ILE A 27 ASP A 57 TRP A 71 SITE 2 AC5 7 LYS A 191 GOL A 202 HOH A 309 SITE 1 AC6 6 HIS A 39 THR A 151 GLY A 152 ASP A 165 SITE 2 AC6 6 GLY A 167 HOH A 339 CRYST1 35.470 63.100 41.870 90.00 98.31 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 0.028193 0.000000 0.004118 0.00000 SCALE2 0.000000 0.015848 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024137 0.00000