HEADER OXIDOREDUCTASE 03-AUG-13 2MBS TITLE NMR SOLUTION STRUCTURE OF OXIDIZED KPDSBA COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 20-207; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 507522; SOURCE 4 STRAIN: 342; SOURCE 5 GENE: DSBA, KPK_5512; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA-2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PMCSG-KPDSBA KEYWDS OXIDOREDUCTASE, THIOREDOXIN DOMAIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.KURTH,K.RIMMER,L.PREMKUMAR,B.MOHANTY,W.DUPREZ,M.A.HALILI, AUTHOR 2 S.R.SHOULDICE,B.HERAS,D.P.FAIRLIE,M.J.SCANLON,J.L.MARTIN REVDAT 2 14-JUN-23 2MBS 1 REMARK SEQADV REVDAT 1 11-DEC-13 2MBS 0 JRNL AUTH F.KURTH,K.RIMMER,L.PREMKUMAR,B.MOHANTY,W.DUPREZ,M.A.HALILI, JRNL AUTH 2 S.R.SHOULDICE,B.HERAS,D.P.FAIRLIE,M.J.SCANLON,J.L.MARTIN JRNL TITL COMPARATIVE SEQUENCE, STRUCTURE AND REDOX ANALYSES OF JRNL TITL 2 KLEBSIELLA PNEUMONIAE DSBA SHOW THAT ANTI-VIRULENCE TARGET JRNL TITL 3 DSBA ENZYMES FALL INTO DISTINCT CLASSES. JRNL REF PLOS ONE V. 8 80210 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 24244651 JRNL DOI 10.1371/JOURNAL.PONE.0080210 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.0, OPALP REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 LUGINBUHL, GUNTERT, BILLETER AND WUTHRICH (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MBS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000103450. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM [U-100% 13C; U-100% 15N] REMARK 210 KPDSBA, 50 MM SODIUM PHOSPHATE, REMARK 210 2 MM EDTA, 0.02 % SODIUM AZIDE, REMARK 210 10 % [U-100% 2H] D2O, 1 MM DSS, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HBHA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UNIO REMARK 210 METHOD USED : WATER REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 CYS A 30 CA - CB - SG ANGL. DEV. = 10.3 DEGREES REMARK 500 2 PHE A 28 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 PHE A 28 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 CYS A 30 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 2 TYR A 59 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 ARG A 108 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 3 PHE A 25 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES REMARK 500 4 CYS A 30 CA - CB - SG ANGL. DEV. = 8.4 DEGREES REMARK 500 11 PHE A 28 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 11 PHE A 28 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 12 CYS A 30 CA - CB - SG ANGL. DEV. = 7.2 DEGREES REMARK 500 14 VAL A 154 CA - CB - CG1 ANGL. DEV. = 21.6 DEGREES REMARK 500 16 PHE A 28 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES REMARK 500 16 CYS A 30 CA - CB - SG ANGL. DEV. = 8.7 DEGREES REMARK 500 17 CYS A 30 CA - CB - SG ANGL. DEV. = 9.1 DEGREES REMARK 500 20 PHE A 28 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 20 PHE A 28 CB - CG - CD1 ANGL. DEV. = 4.4 DEGREES 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 1 ASN A 0 166.01 70.22 REMARK 500 1 GLN A 2 116.77 -166.20 REMARK 500 1 LYS A 7 -86.48 -100.63 REMARK 500 1 ALA A 17 -176.93 65.51 REMARK 500 1 GLU A 19 166.50 61.23 REMARK 500 1 GLU A 38 -36.37 -139.58 REMARK 500 1 VAL A 39 -76.84 -102.56 REMARK 500 1 GLU A 52 40.85 -84.75 REMARK 500 1 LYS A 55 126.72 57.87 REMARK 500 1 LYS A 58 104.80 -166.70 REMARK 500 1 PHE A 63 1.09 -60.92 REMARK 500 1 GLN A 102 -26.61 -144.35 REMARK 500 1 GLU A 138 11.67 -68.87 REMARK 500 1 ASN A 155 24.12 44.88 REMARK 500 1 LYS A 157 -3.55 -150.24 REMARK 500 1 MET A 170 -53.94 75.47 REMARK 500 2 ASN A 0 -10.18 75.79 REMARK 500 2 ALA A 1 48.74 -76.31 REMARK 500 2 LYS A 7 -77.35 -91.80 REMARK 500 2 ALA A 17 -173.69 50.65 REMARK 500 2 GLU A 19 166.39 60.74 REMARK 500 2 PRO A 20 64.68 -67.61 REMARK 500 2 GLN A 21 -28.64 54.06 REMARK 500 2 GLU A 38 -35.07 -138.38 REMARK 500 2 VAL A 39 -78.79 -111.05 REMARK 500 2 GLU A 52 45.44 -76.97 REMARK 500 2 LYS A 55 90.94 44.66 REMARK 500 2 MET A 56 105.57 -58.33 REMARK 500 2 GLN A 102 -25.06 -145.84 REMARK 500 2 ALA A 105 8.48 -62.16 REMARK 500 2 ASP A 143 -85.68 -56.05 REMARK 500 2 LEU A 144 41.49 179.18 REMARK 500 2 GLN A 145 -45.27 -133.56 REMARK 500 2 LEU A 146 -85.30 -85.11 REMARK 500 2 LYS A 157 -10.40 -160.52 REMARK 500 2 THR A 167 32.51 -73.65 REMARK 500 2 MET A 170 -52.53 65.49 REMARK 500 2 LYS A 187 70.76 -104.80 REMARK 500 3 GLN A 2 107.36 -161.10 REMARK 500 3 LYS A 7 -84.80 -89.72 REMARK 500 3 ALA A 17 -43.28 -151.68 REMARK 500 3 VAL A 22 91.68 51.41 REMARK 500 3 HIS A 32 -48.28 69.04 REMARK 500 3 GLU A 38 -26.40 -142.71 REMARK 500 3 LYS A 55 86.64 50.14 REMARK 500 3 LYS A 58 103.51 -176.81 REMARK 500 3 LEU A 67 22.38 -75.37 REMARK 500 3 ASP A 143 -85.77 -57.31 REMARK 500 3 LEU A 144 43.03 174.74 REMARK 500 3 LEU A 146 -85.96 -127.73 REMARK 500 REMARK 500 THIS ENTRY HAS 346 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 16 ALA A 17 9 147.74 REMARK 500 ALA A 140 ALA A 141 12 149.38 REMARK 500 THR A 54 LYS A 55 18 -149.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 TYR A 29 0.12 SIDE CHAIN REMARK 500 1 TYR A 34 0.14 SIDE CHAIN REMARK 500 2 TYR A 34 0.10 SIDE CHAIN REMARK 500 2 TYR A 153 0.09 SIDE CHAIN REMARK 500 3 TYR A 34 0.08 SIDE CHAIN REMARK 500 4 TYR A 29 0.11 SIDE CHAIN REMARK 500 5 TYR A 34 0.12 SIDE CHAIN REMARK 500 6 TYR A 34 0.12 SIDE CHAIN REMARK 500 6 ARG A 47 0.10 SIDE CHAIN REMARK 500 9 TYR A 34 0.10 SIDE CHAIN REMARK 500 9 TYR A 121 0.10 SIDE CHAIN REMARK 500 9 TYR A 158 0.07 SIDE CHAIN REMARK 500 10 PHE A 25 0.07 SIDE CHAIN REMARK 500 10 TYR A 34 0.13 SIDE CHAIN REMARK 500 10 TYR A 59 0.07 SIDE CHAIN REMARK 500 11 TYR A 29 0.10 SIDE CHAIN REMARK 500 11 TYR A 34 0.12 SIDE CHAIN REMARK 500 11 TYR A 153 0.16 SIDE CHAIN REMARK 500 12 TYR A 9 0.07 SIDE CHAIN REMARK 500 12 TYR A 34 0.11 SIDE CHAIN REMARK 500 13 TYR A 34 0.10 SIDE CHAIN REMARK 500 13 TYR A 153 0.08 SIDE CHAIN REMARK 500 14 TYR A 34 0.10 SIDE CHAIN REMARK 500 15 PHE A 25 0.08 SIDE CHAIN REMARK 500 15 TYR A 34 0.10 SIDE CHAIN REMARK 500 16 TYR A 29 0.18 SIDE CHAIN REMARK 500 16 TYR A 34 0.07 SIDE CHAIN REMARK 500 16 TYR A 121 0.08 SIDE CHAIN REMARK 500 16 TYR A 177 0.07 SIDE CHAIN REMARK 500 17 TYR A 29 0.10 SIDE CHAIN REMARK 500 17 TYR A 34 0.09 SIDE CHAIN REMARK 500 17 TYR A 153 0.15 SIDE CHAIN REMARK 500 19 TYR A 153 0.07 SIDE CHAIN REMARK 500 20 TYR A 29 0.13 SIDE CHAIN REMARK 500 20 TYR A 34 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19413 RELATED DB: BMRB REMARK 900 RELATED ID: 2MBT RELATED DB: PDB REMARK 900 RELATED ID: 4MCU RELATED DB: PDB DBREF 2MBS A 1 188 UNP B5XZJ6 B5XZJ6_KLEP3 20 207 SEQADV 2MBS SER A -1 UNP B5XZJ6 EXPRESSION TAG SEQADV 2MBS ASN A 0 UNP B5XZJ6 EXPRESSION TAG SEQRES 1 A 190 SER ASN ALA GLN ILE THR ASP GLY LYS GLN TYR ILE THR SEQRES 2 A 190 LEU ASP LYS PRO ILE ALA GLY GLU PRO GLN VAL LEU GLU SEQRES 3 A 190 PHE PHE SER PHE TYR CYS PRO HIS CYS TYR GLN PHE GLU SEQRES 4 A 190 GLU VAL LEU HIS VAL SER ASP ASN VAL ARG GLN LYS LEU SEQRES 5 A 190 PRO GLU GLY THR LYS MET THR LYS TYR HIS VAL GLU PHE SEQRES 6 A 190 LEU GLY PRO LEU GLY LYS ASP LEU THR GLN ALA TRP ALA SEQRES 7 A 190 VAL ALA ILE ALA LEU GLY VAL GLU ASP LYS ILE THR ALA SEQRES 8 A 190 PRO MET PHE GLU ALA VAL GLN LYS THR GLN THR VAL GLN SEQRES 9 A 190 SER VAL ALA ASP ILE ARG LYS VAL PHE VAL ASP ALA GLY SEQRES 10 A 190 VAL LYS GLY GLU ASP TYR ASP ALA ALA TRP ASN SER PHE SEQRES 11 A 190 VAL VAL LYS SER LEU VAL ALA GLN GLN GLU LYS ALA ALA SEQRES 12 A 190 ALA ASP LEU GLN LEU GLN GLY VAL PRO ALA MET TYR VAL SEQRES 13 A 190 ASN GLY LYS TYR GLN LEU ASN PRO GLN GLY MET ASP THR SEQRES 14 A 190 SER ASN MET ASP VAL PHE VAL ALA GLN TYR ALA ASP THR SEQRES 15 A 190 VAL LYS GLN LEU VAL GLU LYS LYS HELIX 1 1 CYS A 30 VAL A 39 1 10 HELIX 2 2 HIS A 41 GLN A 48 1 8 HELIX 3 3 LEU A 67 GLY A 82 1 16 HELIX 4 4 GLU A 84 ILE A 87 5 4 HELIX 5 5 THR A 88 GLN A 96 1 9 HELIX 6 6 SER A 103 GLY A 115 1 13 HELIX 7 7 LYS A 117 TRP A 125 1 9 HELIX 8 8 SER A 127 ALA A 141 1 15 HELIX 9 9 MET A 170 LYS A 187 1 18 SHEET 1 A 4 TYR A 9 THR A 11 0 SHEET 2 A 4 TYR A 158 LEU A 160 -1 O GLN A 159 N ILE A 10 SHEET 3 A 4 ALA A 151 VAL A 154 -1 N VAL A 154 O TYR A 158 SHEET 4 A 4 GLU A 24 PHE A 25 -1 N PHE A 25 O ALA A 151 SSBOND 1 CYS A 30 CYS A 33 1555 1555 2.04 CISPEP 1 VAL A 149 PRO A 150 1 -10.14 CISPEP 2 VAL A 149 PRO A 150 2 -8.76 CISPEP 3 VAL A 149 PRO A 150 3 -5.50 CISPEP 4 VAL A 149 PRO A 150 4 -11.51 CISPEP 5 VAL A 149 PRO A 150 5 -10.62 CISPEP 6 VAL A 149 PRO A 150 6 -9.12 CISPEP 7 VAL A 149 PRO A 150 7 -0.19 CISPEP 8 VAL A 149 PRO A 150 8 -4.51 CISPEP 9 VAL A 149 PRO A 150 9 -13.83 CISPEP 10 VAL A 149 PRO A 150 10 -14.08 CISPEP 11 VAL A 149 PRO A 150 11 -14.68 CISPEP 12 VAL A 149 PRO A 150 12 -13.31 CISPEP 13 VAL A 149 PRO A 150 13 -9.16 CISPEP 14 VAL A 149 PRO A 150 14 -11.93 CISPEP 15 VAL A 149 PRO A 150 15 -21.54 CISPEP 16 VAL A 149 PRO A 150 16 -6.84 CISPEP 17 VAL A 149 PRO A 150 17 -10.86 CISPEP 18 VAL A 149 PRO A 150 18 -19.38 CISPEP 19 VAL A 149 PRO A 150 19 -8.53 CISPEP 20 VAL A 149 PRO A 150 20 -4.72 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1