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- PDB-1tjd: The crystal structure of the reduced disulphide bond isomerase, D... -

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Basic information

Entry
Database: PDB / ID: 1tjd
TitleThe crystal structure of the reduced disulphide bond isomerase, DsbC, from Escherichia coli
ComponentsThiol:disulfide interchange protein dsbC
KeywordsISOMERASE / dimer
Function / homology
Function and homology information


response to copper ion / protein disulfide isomerase activity / protein-disulfide reductase activity / chaperone-mediated protein folding / outer membrane-bounded periplasmic space / periplasmic space / protein homodimerization activity
Similarity search - Function
Disulphide bond isomerase, DsbC/G, N-terminal / Disulfide bond isomerase protein N-terminus / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G / Thioredoxin-like domain / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. ...Disulphide bond isomerase, DsbC/G, N-terminal / Disulfide bond isomerase protein N-terminus / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G / Thioredoxin-like domain / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Nuclear Transport Factor 2; Chain: A, / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbC / Thiol:disulfide interchange protein DsbC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBanaszak, K. / Mechin, I. / Frost, G. / Rypniewski, W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the reduced disulfide-bond isomerase DsbC from Escherichia coli.
Authors: Banaszak, K. / Mechin, I. / Frost, G. / Rypniewski, W.
History
DepositionJun 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein dsbC


Theoretical massNumber of molelcules
Total (without water)23,4881
Polymers23,4881
Non-polymers00
Water1,27971
1
A: Thiol:disulfide interchange protein dsbC

A: Thiol:disulfide interchange protein dsbC


Theoretical massNumber of molelcules
Total (without water)46,9762
Polymers46,9762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)41.897, 145.799, 73.582
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -X, Y, Z-1/2

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Components

#1: Protein Thiol:disulfide interchange protein dsbC


Mass: 23488.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DSBC, XPRA, B2893, Z4231, ECS3765 / Plasmid: pDM801 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE2)
References: UniProt: P21892, UniProt: P0AEG6*PLUS, protein disulfide-isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.2 M LiSO4, 0.1 M Tris pH 8.4 and 20% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.906 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 19, 1998
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.906 Å / Relative weight: 1
ReflectionResolution: 2.5→17 Å / Num. all: 8103 / Num. obs: 7953 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 14
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.6 / Num. unique all: 435 / Rsym value: 0.386 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EEJ

1eej


Resolution: 2.5→16.74 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.896 / SU B: 8.374 / SU ML: 0.19 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.576 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26964 150 1.9 %RANDOM
Rwork0.2031 ---
all0.2043 8103 --
obs0.2043 7953 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.045 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--0.59 Å20 Å2
3----0.98 Å2
Refine analyzeLuzzati sigma a obs: 0.1898 Å
Refinement stepCycle: LAST / Resolution: 2.5→16.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 0 71 1714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221621
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9612203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8015214
X-RAY DIFFRACTIONr_chiral_restr0.0750.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021208
X-RAY DIFFRACTIONr_nbd_refined0.20.2703
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.25
X-RAY DIFFRACTIONr_mcbond_it0.6191.51070
X-RAY DIFFRACTIONr_mcangle_it1.21321716
X-RAY DIFFRACTIONr_scbond_it2.0943551
X-RAY DIFFRACTIONr_scangle_it3.284.5487
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 7 -
Rwork0.222 566 -
obs-566 100 %

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