HEADER OXIDOREDUCTASE 01-MAY-15 4ZL7 TITLE CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA DSBA E82I: CRYSTAL I COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 22-211; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: THE FIRST THREE RESIDUES (SNA) DERIVE FROM AN COMPND 8 EXPRESSION TAG 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 4ZL7 1 REMARK REVDAT 3 01-JAN-20 4ZL7 1 REMARK REVDAT 2 18-APR-18 4ZL7 1 JRNL REMARK REVDAT 1 09-DEC-15 4ZL7 0 JRNL AUTH R.M.MCMAHON,M.COINCON,S.TAY,B.HERAS,C.J.MORTON,M.J.SCANLON, JRNL AUTH 2 J.L.MARTIN JRNL TITL SENT PACKING: PROTEIN ENGINEERING GENERATES A NEW CRYSTAL JRNL TITL 2 FORM OF PSEUDOMONAS AERUGINOSA DSBA1 WITH INCREASED JRNL TITL 3 CATALYTIC SURFACE ACCESSIBILITY. JRNL REF ACTA CRYSTALLOGR. D BIOL. V. 71 2386 2015 JRNL REF 2 CRYSTALLOGR. JRNL REFN ESSN 1399-0047 JRNL PMID 26627647 JRNL DOI 10.1107/S1399004715018519 REMARK 2 REMARK 2 RESOLUTION. 1.92 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 13653 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 687 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 41.2676 - 3.2863 1.00 2643 137 0.1537 0.1514 REMARK 3 2 3.2863 - 2.6085 0.99 2571 144 0.1608 0.2247 REMARK 3 3 2.6085 - 2.2788 0.99 2607 125 0.1564 0.2596 REMARK 3 4 2.2788 - 2.0705 1.00 2559 140 0.1594 0.2368 REMARK 3 5 2.0705 - 1.9220 1.00 2586 141 0.1836 0.2349 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.38 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 1541 REMARK 3 ANGLE : 1.341 2087 REMARK 3 CHIRALITY : 0.073 222 REMARK 3 PLANARITY : 0.006 265 REMARK 3 DIHEDRAL : 14.856 576 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 5 THROUGH 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 77.4136 -11.6081 40.5682 REMARK 3 T TENSOR REMARK 3 T11: 0.1284 T22: 0.0777 REMARK 3 T33: 0.1039 T12: -0.0059 REMARK 3 T13: -0.0103 T23: -0.0155 REMARK 3 L TENSOR REMARK 3 L11: 2.4219 L22: 1.4815 REMARK 3 L33: 0.5189 L12: -1.0813 REMARK 3 L13: -0.2342 L23: -0.3158 REMARK 3 S TENSOR REMARK 3 S11: -0.0611 S12: -0.0295 S13: -0.1217 REMARK 3 S21: -0.0637 S22: -0.0226 S23: 0.0683 REMARK 3 S31: 0.0216 S32: 0.0241 S33: 0.0892 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 69 THROUGH 148 ) REMARK 3 ORIGIN FOR THE GROUP (A): 67.1435 -2.3514 53.8184 REMARK 3 T TENSOR REMARK 3 T11: 0.1048 T22: 0.0971 REMARK 3 T33: 0.1165 T12: 0.0053 REMARK 3 T13: -0.0058 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 1.6713 L22: 2.4164 REMARK 3 L33: 3.4091 L12: 0.7058 REMARK 3 L13: -0.2026 L23: 0.2501 REMARK 3 S TENSOR REMARK 3 S11: 0.1272 S12: -0.1441 S13: 0.0059 REMARK 3 S21: 0.2630 S22: -0.0421 S23: 0.0328 REMARK 3 S31: -0.0088 S32: -0.0693 S33: -0.0639 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 149 THROUGH 189 ) REMARK 3 ORIGIN FOR THE GROUP (A): 79.1960 -14.7395 34.8755 REMARK 3 T TENSOR REMARK 3 T11: 0.1194 T22: 0.0894 REMARK 3 T33: 0.0813 T12: -0.0099 REMARK 3 T13: -0.0060 T23: -0.0169 REMARK 3 L TENSOR REMARK 3 L11: 5.6973 L22: 4.0137 REMARK 3 L33: 2.6858 L12: 0.1884 REMARK 3 L13: -0.3307 L23: 0.9482 REMARK 3 S TENSOR REMARK 3 S11: 0.1582 S12: 0.2150 S13: -0.2948 REMARK 3 S21: -0.2445 S22: -0.0716 S23: 0.1089 REMARK 3 S31: 0.1200 S32: 0.0502 S33: -0.0264 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 4ZL7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000209473. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-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 : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13668 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 41.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08100 REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.40500 REMARK 200 R SYM FOR SHELL (I) : 0.40500 REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.0 REMARK 200 STARTING MODEL: 3H93 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 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 31.15500 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 ALA A 190 REMARK 465 LYS A 191 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 O HOH A 391 O HOH A 405 2.03 REMARK 500 OH TYR A 41 NZ LYS A 100 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 -83.11 -107.21 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 P6G A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3H93 RELATED DB: PDB REMARK 900 3H93 CONTAINS THE WILD TYPE SEQUENCE OF THIS PROTEIN REMARK 900 RELATED ID: 2MBT RELATED DB: PDB REMARK 900 2MBT CONTAINS THE NMR SOLUTION STRUCTURE OF THE WILD TYPE SEQUENCE REMARK 900 OF THIS PROTEIN REMARK 900 RELATED ID: 4ZL8 RELATED DB: PDB REMARK 900 RELATED ID: 4ZL9 RELATED DB: PDB DBREF 4ZL7 A 3 192 UNP P0C2B2 DSBA_PSEAE 22 211 SEQADV 4ZL7 SER A 1 UNP P0C2B2 EXPRESSION TAG SEQADV 4ZL7 ASN A 2 UNP P0C2B2 EXPRESSION TAG SEQADV 4ZL7 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 P6G A 201 19 HETNAM P6G HEXAETHYLENE GLYCOL HETSYN P6G POLYETHYLENE GLYCOL PEG400 FORMUL 2 P6G C12 H26 O7 FORMUL 3 HOH *111(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 188 1 18 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 VAL A 30 O VAL A 157 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 2.02 CISPEP 1 VAL A 153 PRO A 154 0 -6.25 SITE 1 AC1 3 PRO A 49 TRP A 50 LYS A 53 CRYST1 35.340 62.310 41.620 90.00 97.56 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 0.028297 0.000000 0.003755 0.00000 SCALE2 0.000000 0.016049 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024238 0.00000