10 20 30 40 50 60 70 80 2B5X - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 29-SEP-05 2B5X
TITLE SOLUTION STRUCTURE OF A THIOREDOXIN-LIKE PROTEIN IN THE TITLE 2 REDUCED FORM
COMPND MOL_ID: 1; COMPND 2 MOLECULE: YKUV PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-148; COMPND 5 SYNONYM: TRXY; COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21A
KEYWDS THIOREDOXIN-LIKE, OXIDOREDUCTASE
EXPDTA SOLUTION NMR
NUMMDL 11
MDLTYP MINIMIZED AVERAGE
AUTHOR X.ZHANG,B.XIA,C.JIN
REVDAT 3 24-FEB-09 2B5X 1 VERSN REVDAT 2 28-MAR-06 2B5X 1 JRNL REVDAT 1 17-JAN-06 2B5X 0
JRNL AUTH X.ZHANG,Y.HU,X.GUO,E.LESCOP,Y.LI,B.XIA,C.JIN JRNL TITL THE BACILLUS SUBTILIS YKUV IS A THIOL-DISULFIDE JRNL TITL 2 OXIDOREDUCTASE REVEALED BY ITS REDOX STRUCTURES JRNL TITL 3 AND ACTIVITY JRNL REF J.BIOL.CHEM. V. 281 8296 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16418167 JRNL DOI 10.1074/JBC.M512015200
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 REMARK 3 AUTHORS : D.CASE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2B5X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-OCT-05. REMARK 100 THE RCSB ID CODE IS RCSB034714.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.4 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 50MM SODIUM PHOSPHATE, 100MM REMARK 210 SODIUM CHLORIDE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM TRXY U-15N, 13C; 50MM REMARK 210 SODIUM PHOSPHATE, 100MM SODIUM REMARK 210 CHLORIDE; 90% H2O 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY, 3D_ REMARK 210 15N-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, SANE, CYANA REMARK 210 1.0.6, NMRVIEW 5, XWINNMR 3.5 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 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: ENSEMBLED STRUCTURES PLUS MEAN STRUCTURE
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 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 3 ARG A 124 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 7 ARG A 142 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 11 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.8 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 PRO A 8 -102.41 -92.59 REMARK 500 1 GLU A 13 -29.02 -158.65 REMARK 500 1 ASN A 18 -33.31 68.83 REMARK 500 1 GLU A 29 -42.79 -138.58 REMARK 500 1 ARG A 71 -33.25 -139.06 REMARK 500 1 GLU A 109 37.75 -157.52 REMARK 500 2 LYS A 2 -126.19 -124.74 REMARK 500 2 PRO A 8 -154.27 -82.24 REMARK 500 2 TRP A 16 54.12 -149.06 REMARK 500 2 ASN A 18 -30.23 69.35 REMARK 500 2 GLU A 29 -40.13 -148.83 REMARK 500 2 ARG A 71 -31.25 -140.55 REMARK 500 2 ASP A 75 -13.56 -142.11 REMARK 500 2 ASP A 99 -46.77 -134.02 REMARK 500 2 HIS A 100 130.39 67.27 REMARK 500 2 ASN A 108 119.33 -34.23 REMARK 500 2 GLU A 109 43.00 -150.22 REMARK 500 2 VAL A 111 141.48 -175.74 REMARK 500 2 SER A 131 109.07 -52.11 REMARK 500 3 ARG A 4 13.84 51.96 REMARK 500 3 PRO A 8 -144.91 -88.15 REMARK 500 3 ASN A 18 -31.61 72.54 REMARK 500 3 ARG A 23 8.94 -61.40 REMARK 500 3 GLU A 29 -51.66 -152.46 REMARK 500 3 PRO A 31 170.79 -55.02 REMARK 500 3 ASP A 99 -38.26 -130.64 REMARK 500 3 HIS A 100 95.14 62.06 REMARK 500 3 ASN A 108 118.34 -37.16 REMARK 500 3 GLU A 109 47.67 -144.09 REMARK 500 3 VAL A 111 145.36 -178.23 REMARK 500 3 LEU A 123 92.55 -59.33 REMARK 500 3 MET A 133 29.19 -143.49 REMARK 500 3 THR A 147 45.24 -145.77 REMARK 500 4 ARG A 4 16.64 56.41 REMARK 500 4 PRO A 8 -139.60 -87.92 REMARK 500 4 LEU A 10 91.64 -59.08 REMARK 500 4 TRP A 16 55.53 -141.27 REMARK 500 4 ASN A 18 -30.99 72.97 REMARK 500 4 GLU A 29 -46.59 -144.72 REMARK 500 4 PRO A 31 164.58 -46.68 REMARK 500 4 ARG A 71 -32.20 -138.19 REMARK 500 4 HIS A 100 100.35 54.03 REMARK 500 4 GLU A 109 31.75 -149.33 REMARK 500 4 VAL A 111 145.76 -173.37 REMARK 500 4 LYS A 119 -5.24 -59.79 REMARK 500 4 LEU A 123 106.84 -58.14 REMARK 500 4 MET A 133 15.55 -141.51 REMARK 500 4 THR A 147 44.57 -140.01 REMARK 500 5 PRO A 8 -139.67 -92.71 REMARK 500 5 GLU A 13 -27.27 -143.41 REMARK 500 5 TRP A 16 54.29 -145.29 REMARK 500 5 ASN A 18 -33.73 68.35 REMARK 500 5 ARG A 23 12.47 -64.63 REMARK 500 5 GLU A 29 -50.23 -153.42 REMARK 500 5 ARG A 71 -36.57 -139.78 REMARK 500 5 HIS A 100 87.84 53.67 REMARK 500 5 GLU A 109 40.90 -154.92 REMARK 500 5 SER A 131 29.57 49.33 REMARK 500 5 MET A 133 29.65 48.23 REMARK 500 5 THR A 147 45.02 -140.96 REMARK 500 6 PRO A 8 -79.33 -90.74 REMARK 500 6 GLU A 13 89.64 -152.99 REMARK 500 6 LYS A 14 -44.41 -139.50 REMARK 500 6 ASN A 18 -30.86 71.82 REMARK 500 6 GLU A 29 -45.33 -145.20 REMARK 500 6 PRO A 31 164.32 -48.78 REMARK 500 6 SER A 72 -146.03 -144.07 REMARK 500 6 ASP A 75 7.02 -67.28 REMARK 500 6 HIS A 100 91.66 55.42 REMARK 500 6 ASN A 108 123.50 -39.47 REMARK 500 6 GLU A 109 19.22 -142.80 REMARK 500 7 ARG A 4 14.35 54.03 REMARK 500 7 PRO A 8 -157.06 -76.86 REMARK 500 7 TRP A 16 52.24 -141.35 REMARK 500 7 ASN A 18 -34.77 74.17 REMARK 500 7 ARG A 23 10.73 -63.42 REMARK 500 7 GLU A 29 -53.29 -136.66 REMARK 500 7 ASP A 99 -37.19 -138.36 REMARK 500 7 HIS A 100 123.35 64.67 REMARK 500 7 GLU A 109 27.89 -153.31 REMARK 500 7 LEU A 123 95.87 -62.93 REMARK 500 7 SER A 131 109.72 -51.29 REMARK 500 7 THR A 147 45.11 -140.83 REMARK 500 8 PRO A 8 -72.16 -80.33 REMARK 500 8 ASN A 18 -31.16 71.81 REMARK 500 8 GLU A 29 -41.77 -156.11 REMARK 500 8 GLN A 61 -16.31 -142.84 REMARK 500 8 ILE A 90 98.37 -63.05 REMARK 500 8 ASP A 99 -32.65 -131.81 REMARK 500 8 HIS A 100 98.79 54.01 REMARK 500 8 GLU A 109 33.00 -148.69 REMARK 500 8 SER A 131 109.20 -51.56 REMARK 500 8 MET A 133 23.24 49.59 REMARK 500 8 THR A 147 45.41 -141.05 REMARK 500 9 ARG A 4 15.56 57.21 REMARK 500 9 PRO A 8 -85.41 -85.95 REMARK 500 9 GLU A 13 -18.95 -140.19 REMARK 500 9 ASN A 18 -29.87 70.61 REMARK 500 9 GLU A 29 -45.35 -147.49 REMARK 500 9 ILE A 39 20.69 -72.34 REMARK 500 9 GLN A 61 -14.93 -140.47 REMARK 500 9 ARG A 71 -34.99 -138.62 REMARK 500 9 HIS A 100 80.86 53.85 REMARK 500 9 GLU A 109 36.85 -157.35 REMARK 500 9 LEU A 123 95.48 -55.87 REMARK 500 9 SER A 131 109.27 -53.17 REMARK 500 9 ALA A 145 2.78 -68.89 REMARK 500 10 LEU A 3 133.06 -25.38 REMARK 500 10 MET A 7 121.66 -39.89 REMARK 500 10 PRO A 8 -142.22 -102.25 REMARK 500 10 GLU A 9 58.38 -66.57 REMARK 500 10 LEU A 10 101.93 -59.81 REMARK 500 10 ASN A 18 -25.65 68.95 REMARK 500 10 GLU A 29 -44.09 -153.37 REMARK 500 10 GLN A 61 -14.95 -143.29 REMARK 500 10 HIS A 100 91.25 61.57 REMARK 500 10 GLU A 109 32.54 -145.57 REMARK 500 10 LYS A 119 -1.36 -56.77 REMARK 500 10 SER A 131 105.56 -54.84 REMARK 500 10 MET A 133 19.98 52.04 REMARK 500 11 LYS A 2 155.04 64.71 REMARK 500 11 LEU A 3 95.39 50.14 REMARK 500 11 MET A 7 121.43 -27.72 REMARK 500 11 ASN A 18 -7.89 62.55 REMARK 500 11 ARG A 23 13.33 -67.08 REMARK 500 11 GLN A 25 -32.55 -132.08 REMARK 500 11 GLU A 29 -41.62 -146.92 REMARK 500 11 ASP A 99 -38.44 -135.98 REMARK 500 11 HIS A 100 125.77 67.90 REMARK 500 11 GLU A 109 41.85 -155.76 REMARK 500 11 LEU A 123 91.08 -68.45 REMARK 500 11 THR A 147 44.77 -143.15 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 ARG A 55 0.09 SIDE_CHAIN REMARK 500 3 TYR A 58 0.07 SIDE_CHAIN REMARK 500 3 TYR A 114 0.07 SIDE_CHAIN REMARK 500 4 PHE A 54 0.08 SIDE_CHAIN REMARK 500 4 TYR A 110 0.08 SIDE_CHAIN REMARK 500 5 TYR A 58 0.08 SIDE_CHAIN REMARK 500 8 ARG A 139 0.09 SIDE_CHAIN REMARK 500 9 TYR A 110 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6603 RELATED DB: BMRB
DBREF 2B5X A 1 148 GB 2632243 CAA10885 1 148
SEQADV 2B5X LEU A 144 GB 2632243 TRP 144 ENGINEERED SEQADV 2B5X ALA A 145 GB 2632243 LEU 145 ENGINEERED SEQADV 2B5X GLU A 146 GB 2632243 LYS 146 ENGINEERED SEQADV 2B5X THR A 147 GB 2632243 ARG 147 ENGINEERED SEQADV 2B5X GLU A 148 GB 2632243 ASN 148 ENGINEERED
SEQRES 1 A 148 MET LYS LEU ARG GLN PRO MET PRO GLU LEU THR GLY GLU SEQRES 2 A 148 LYS ALA TRP LEU ASN GLY GLU VAL THR ARG GLU GLN LEU SEQRES 3 A 148 ILE GLY GLU LYS PRO THR LEU ILE HIS PHE TRP SER ILE SEQRES 4 A 148 SER CYS HIS LEU CYS LYS GLU ALA MET PRO GLN VAL ASN SEQRES 5 A 148 GLU PHE ARG ASP LYS TYR GLN ASP GLN LEU ASN VAL VAL SEQRES 6 A 148 ALA VAL HIS MET PRO ARG SER GLU ASP ASP LEU ASP PRO SEQRES 7 A 148 GLY LYS ILE LYS GLU THR ALA ALA GLU HIS ASP ILE THR SEQRES 8 A 148 GLN PRO ILE PHE VAL ASP SER ASP HIS ALA LEU THR ASP SEQRES 9 A 148 ALA PHE GLU ASN GLU TYR VAL PRO ALA TYR TYR VAL PHE SEQRES 10 A 148 ASP LYS THR GLY GLN LEU ARG HIS PHE GLN ALA GLY GLY SEQRES 11 A 148 SER GLY MET LYS MET LEU GLU LYS ARG VAL ASN ARG VAL SEQRES 12 A 148 LEU ALA GLU THR GLU
HELIX 1 1 THR A 22 ILE A 27 1 6 HELIX 2 2 CYS A 41 GLN A 59 1 19 HELIX 3 3 ASP A 77 HIS A 88 1 12 HELIX 4 4 HIS A 100 PHE A 106 1 7 HELIX 5 5 MET A 133 ALA A 145 1 13
SHEET 1 A 6 TRP A 16 LEU A 17 0 SHEET 2 A 6 ILE A 94 VAL A 96 -1 O ILE A 94 N LEU A 17 SHEET 3 A 6 ASN A 63 HIS A 68 1 N HIS A 68 O PHE A 95 SHEET 4 A 6 THR A 32 TRP A 37 1 N LEU A 33 O ASN A 63 SHEET 5 A 6 ALA A 113 PHE A 117 -1 O TYR A 115 N ILE A 34 SHEET 6 A 6 LEU A 123 ALA A 128 -1 O ARG A 124 N VAL A 116
CISPEP 1 VAL A 111 PRO A 112 1 -20.97 CISPEP 2 VAL A 111 PRO A 112 2 -11.56 CISPEP 3 VAL A 111 PRO A 112 3 -10.98 CISPEP 4 VAL A 111 PRO A 112 4 -11.39 CISPEP 5 VAL A 111 PRO A 112 5 -11.40 CISPEP 6 VAL A 111 PRO A 112 6 -11.30 CISPEP 7 VAL A 111 PRO A 112 7 -12.07 CISPEP 8 VAL A 111 PRO A 112 8 -11.01 CISPEP 9 VAL A 111 PRO A 112 9 -11.91 CISPEP 10 VAL A 111 PRO A 112 10 -11.23 CISPEP 11 VAL A 111 PRO A 112 11 -11.53
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