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- PDB-1bed: STRUCTURE OF DISULFIDE OXIDOREDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1bed
TitleSTRUCTURE OF DISULFIDE OXIDOREDUCTASE
ComponentsDSBA OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / TCPG / PROTEIN DISULFIDE ISOMERASE / DISULFIDE OXIDOREDUCTASE
Function / homology
Function and homology information


periplasmic space / oxidoreductase activity
Similarity search - Function
Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHu, S.-H. / Martin, J.L.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Structure of TcpG, the DsbA protein folding catalyst from Vibrio cholerae.
Authors: Hu, S.H. / Peek, J.A. / Rattigan, E. / Taylor, R.K. / Martin, J.L.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Characterization of a Periplasmic Thiol:Disulfide Interchange Protein Required for the Functional Maturation of Secreted Virulence Factors of Vibrio Cholerae
Authors: Peek, J.A. / Taylor, R.K.
History
DepositionSep 16, 1996Processing site: BNL
Revision 1.0Oct 8, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DSBA OXIDOREDUCTASE


Theoretical massNumber of molelcules
Total (without water)20,5231
Polymers20,5231
Non-polymers00
Water95553
1
A: DSBA OXIDOREDUCTASE

A: DSBA OXIDOREDUCTASE


Theoretical massNumber of molelcules
Total (without water)41,0472
Polymers41,0472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Unit cell
Length a, b, c (Å)64.000, 91.500, 64.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DSBA OXIDOREDUCTASE / TCPG / DISULFIDE BOND FORMATION PROTEIN


Mass: 20523.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria) / References: UniProt: P32557
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.5 / Details: 10-13% EG 4K, 0.1M MES, PH 6.0-6.5 / PH range: 6.0-6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
123 mg/mlprotein1drop
240 mM1dropNaCl
310 mMHEPES1drop
40.5 mMEDTA1drop
510-13 %PEG40001reservoir
60.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 17, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 12974 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.4 / % possible all: 91.7
Reflection
*PLUS
Num. measured all: 60945
Reflection shell
*PLUS
% possible obs: 91.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DSB

1dsb


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.241 931 10 %RANDOM
Rwork0.205 ---
obs0.205 9309 70 %-
Displacement parametersBiso mean: 38.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.24 Å
Luzzati d res low-20 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 0 53 1438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.1→2.2 Å
RfactorNum. reflection% reflection
Rfree0.368 75 5.3 %
Rwork0.277 681 -
obs--54 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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