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- PDB-1v58: Crystal Structure Of the Reduced Protein Disulfide Bond Isomerase DsbG -

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Basic information

Entry
Database: PDB / ID: 1v58
TitleCrystal Structure Of the Reduced Protein Disulfide Bond Isomerase DsbG
ComponentsThiol:disulfide interchange protein dsbG
KeywordsISOMERASE / reduced dsbG / redox protein / protein disulfide isomerase / thioredoxin fold
Function / homology
Function and homology information


protein disulfide isomerase activity / chaperone-mediated protein folding / outer membrane-bounded periplasmic space / protein homodimerization activity
Similarity search - Function
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 / Nuclear Transport Factor 2; Chain: A, / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Roll ...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 / 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 DsbG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsHeras, B. / Edeling, M.A. / Schirra, H.J. / Raina, S. / Martin, J.L.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structures of the DsbG disulfide isomerase reveal an unstable disulfide
Authors: Heras, B. / Edeling, M.A. / Schirra, H.J. / Raina, S. / Martin, J.L.
#1: Journal: Structure / Year: 2003
Title: Dehydration converts DsbG crystal diffraction from low to high resolution.
Authors: Heras, B. / Edeling, M.A. / Byriel, K.A. / Jones, A. / Raina, S. / Martin, J.L.
History
DepositionNov 21, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein dsbG
B: Thiol:disulfide interchange protein dsbG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4806
Polymers54,0962
Non-polymers3844
Water9,908550
1
A: Thiol:disulfide interchange protein dsbG
hetero molecules

A: Thiol:disulfide interchange protein dsbG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4806
Polymers54,0962
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
2
B: Thiol:disulfide interchange protein dsbG
hetero molecules

B: Thiol:disulfide interchange protein dsbG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4806
Polymers54,0962
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)116.541, 57.186, 85.508
Angle α, β, γ (deg.)90.00, 94.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1352-

HOH

DetailsThe biological assembly is a homodimer generated from one momomer in the asymmetric unit by the operations: -x, y, -z.

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Components

#1: Protein Thiol:disulfide interchange protein dsbG / DsbG disulfide bond isomerase


Mass: 27047.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dsbG / Plasmid: pET42b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P77202
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.29 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.75
Details: 20% PEG 4000, 0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9, 0.9783, 0.9785, 0.9556
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 12, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97831
30.97851
40.95561
ReflectionResolution: 1.7→26.55 Å / Num. obs: 57306 / % possible obs: 92.7 % / Observed criterion σ(F): 3 / Redundancy: 6.4 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 30.6
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3289 / % possible all: 53.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→26.55 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Refinement: maximum likelihood in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 5688 -RANDOM
Rwork0.186 ---
all-61856 --
obs-55837 90.1 %-
Displacement parametersBiso mean: 21.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å22.01 Å2
2--0.55 Å20 Å2
3----1.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.7→26.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 20 552 4430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.277 560 -
Rwork0.233 --
obs-5320 57.4 %

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