Header list of 2b5y.pdb file
Complete list - v 10 2 Bytes
HEADER OXIDOREDUCTASE 29-SEP-05 2B5Y
TITLE SOLUTION STRUCTURE OF A THIOREDOXIN-LIKE PROTEIN IN THE OXIDIZED 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 4 10-NOV-21 2B5Y 1 REMARK SEQADV
REVDAT 3 24-FEB-09 2B5Y 1 VERSN
REVDAT 2 28-MAR-06 2B5Y 1 JRNL
REVDAT 1 17-JAN-06 2B5Y 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 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 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRPIPE 2.1, AMBER 7.0
REMARK 3 AUTHORS : F.DELAGLIO, S.GRZESIEK, G.VUISTER, G.ZHU,
REMARK 3 J.PFEIFER, A.BAX (NMRPIPE), D.CASE (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2B5Y COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-OCT-05.
REMARK 100 THE DEPOSITION ID IS D_1000034715.
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 : NULL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1MM TRXY, 50MM SODIUM PHOSPHATE,
REMARK 210 100MM SODIUM CHLORIDE; 90%H2O,
REMARK 210 10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N
REMARK 210 -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 : SANE, CYANA 1.0.6, NMRVIEW 5,
REMARK 210 XWINNMR 3.5
REMARK 210 METHOD USED : SIMULATED ANNEALING MOLECULAR
REMARK 210 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 : 11
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 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 2 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 5 PRO A 112 C - N - CD ANGL. DEV. = -15.5 DEGREES
REMARK 500 5 PRO A 112 CA - N - CD ANGL. DEV. = -9.3 DEGREES
REMARK 500 5 PRO A 112 N - CA - CB ANGL. DEV. = 7.8 DEGREES
REMARK 500 6 PHE A 106 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES
REMARK 500 7 ARG A 23 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 8 PRO A 112 C - N - CD ANGL. DEV. = -15.3 DEGREES
REMARK 500 8 PRO A 112 CA - N - CD ANGL. DEV. = -9.5 DEGREES
REMARK 500 8 PRO A 112 N - CA - CB ANGL. DEV. = 8.0 DEGREES
REMARK 500 9 PRO A 112 C - N - CD ANGL. DEV. = -15.0 DEGREES
REMARK 500 9 PRO A 112 CA - N - CD ANGL. DEV. = -9.7 DEGREES
REMARK 500 9 PRO A 112 N - CA - CB ANGL. DEV. = 7.6 DEGREES
REMARK 500 10 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 10 ARG A 124 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500 11 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.6 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 ARG A 4 -36.67 -163.85
REMARK 500 1 PRO A 8 -169.27 -70.89
REMARK 500 1 ALA A 15 170.69 158.28
REMARK 500 1 ASN A 18 -8.26 58.49
REMARK 500 1 GLU A 29 -13.11 -147.45
REMARK 500 1 SER A 40 27.72 -145.84
REMARK 500 1 ASP A 77 108.41 -56.53
REMARK 500 1 ASP A 99 -53.49 -164.67
REMARK 500 1 HIS A 100 19.06 -164.83
REMARK 500 1 VAL A 111 -58.03 -129.05
REMARK 500 1 MET A 133 28.33 39.39
REMARK 500 2 ARG A 4 -38.19 -161.33
REMARK 500 2 LEU A 10 72.71 -116.23
REMARK 500 2 ALA A 15 174.33 124.63
REMARK 500 2 ASN A 18 8.40 59.28
REMARK 500 2 GLU A 29 -20.76 -143.54
REMARK 500 2 ASP A 77 107.74 -55.87
REMARK 500 2 ASP A 99 82.96 -177.56
REMARK 500 2 VAL A 111 -61.94 -122.56
REMARK 500 2 PRO A 112 85.58 -67.43
REMARK 500 2 SER A 131 105.26 -58.17
REMARK 500 2 MET A 133 19.10 50.76
REMARK 500 2 THR A 147 -171.05 55.25
REMARK 500 3 ARG A 4 -32.21 -170.26
REMARK 500 3 PRO A 8 -179.58 -68.09
REMARK 500 3 ALA A 15 174.65 117.81
REMARK 500 3 ASN A 18 9.53 55.79
REMARK 500 3 GLU A 29 -24.57 -147.82
REMARK 500 3 HIS A 42 9.53 -66.87
REMARK 500 3 ASP A 99 -31.41 -164.24
REMARK 500 3 HIS A 100 -66.44 -155.92
REMARK 500 3 ALA A 101 -93.10 28.72
REMARK 500 3 VAL A 111 -54.59 -126.27
REMARK 500 3 PRO A 112 82.19 -69.43
REMARK 500 3 LYS A 119 12.55 -63.32
REMARK 500 3 SER A 131 100.06 -57.27
REMARK 500 3 MET A 133 28.56 40.29
REMARK 500 4 ARG A 4 -34.49 -165.66
REMARK 500 4 ASN A 18 -0.80 59.47
REMARK 500 4 GLU A 29 -16.88 -144.08
REMARK 500 4 SER A 40 47.00 -144.63
REMARK 500 4 ASP A 60 -5.94 61.36
REMARK 500 4 ASP A 99 -41.79 -170.05
REMARK 500 4 HIS A 100 11.35 -163.57
REMARK 500 4 GLU A 109 -9.43 58.15
REMARK 500 4 PRO A 112 83.88 -69.83
REMARK 500 4 SER A 131 98.86 -59.55
REMARK 500 4 MET A 133 24.09 43.28
REMARK 500 5 ARG A 4 -35.85 -169.37
REMARK 500 5 PRO A 8 -163.30 -77.79
REMARK 500
REMARK 500 THIS ENTRY HAS 133 RAMACHANDRAN OUTLIERS.
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 2 TYR A 115 0.10 SIDE CHAIN
REMARK 500 3 TYR A 115 0.11 SIDE CHAIN
REMARK 500 4 TYR A 115 0.07 SIDE CHAIN
REMARK 500 5 ARG A 55 0.09 SIDE CHAIN
REMARK 500 5 TYR A 115 0.07 SIDE CHAIN
REMARK 500 6 ARG A 23 0.08 SIDE CHAIN
REMARK 500 8 ARG A 23 0.11 SIDE CHAIN
REMARK 500 8 ARG A 71 0.10 SIDE CHAIN
REMARK 500 8 TYR A 115 0.07 SIDE CHAIN
REMARK 500 10 TYR A 115 0.07 SIDE CHAIN
REMARK 500 11 TYR A 114 0.07 SIDE CHAIN
REMARK 500 11 TYR A 115 0.10 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2B5X RELATED DB: PDB
REMARK 900 STRUCTURE IN THE REDUCED FORM
DBREF 2B5Y A 1 148 GB 2632243 CAA10885 1 148
SEQADV 2B5Y LEU A 144 GB 2632243 TRP 144 ENGINEERED MUTATION
SEQADV 2B5Y ALA A 145 GB 2632243 LEU 145 ENGINEERED MUTATION
SEQADV 2B5Y GLU A 146 GB 2632243 LYS 146 ENGINEERED MUTATION
SEQADV 2B5Y THR A 147 GB 2632243 ARG 147 ENGINEERED MUTATION
SEQADV 2B5Y GLU A 148 GB 2632243 ASN 148 ENGINEERED MUTATION
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 LEU A 43 GLN A 59 1 17
HELIX 3 3 SER A 72 LEU A 76 5 5
HELIX 4 4 ASP A 77 HIS A 88 1 12
HELIX 5 5 HIS A 100 PHE A 106 1 7
HELIX 6 6 GLY A 130 MET A 133 5 4
HELIX 7 7 LYS A 134 THR A 147 1 14
SHEET 1 A 6 ALA A 15 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 ALA A 66 O PHE A 95
SHEET 4 A 6 THR A 32 TRP A 37 1 N HIS A 35 O VAL A 67
SHEET 5 A 6 ALA A 113 PHE A 117 -1 O ALA A 113 N PHE A 36
SHEET 6 A 6 LEU A 123 ALA A 128 -1 O ARG A 124 N VAL A 116
SSBOND 1 CYS A 41 CYS A 44 1555 1555 2.04
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
Complete list - v 10 2 Bytes