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- PDB-2h0h: Crystal Structure of DsbG K113E mutant -

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Basic information

Entry
Database: PDB / ID: 2h0h
TitleCrystal Structure of DsbG K113E mutant
ComponentsThiol:disulfide interchange protein dsbG
KeywordsISOMERASE / Thioredoxin fold / Periplasmic disulfide isomerase / Chaperone / Redox-active center
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 / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsHiniker, A. / Heras, B. / Martin, J.L. / Stuckey, J. / Bardwell, J.C.A.
Citation
Journal: To be Published
Title: Short-circuiting divergent evolution: laboratory evolution of one disulfide isomerase to resemble another
Authors: Hiniker, A. / Heras, B. / Jobson, R.W. / Laurinec, S. / Martin, J.L. / Stuckey, J. / Bardwell, J.C.A.
#1: 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.
History
DepositionMay 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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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)53,5417
Polymers53,0612
Non-polymers4805
Water6,413356
1
A: Thiol:disulfide interchange protein dsbG
hetero molecules

A: Thiol:disulfide interchange protein dsbG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4456
Polymers53,0612
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)53,6378
Polymers53,0612
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)117.110, 56.980, 85.003
Angle α, β, γ (deg.)90.00, 94.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-366-

HOH

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Components

#1: Protein Thiol:disulfide interchange protein dsbG


Mass: 26530.344 Da / Num. of mol.: 2 / Fragment: residues 18-248 / Mutation: K113E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dsbG / Plasmid: pBAD33 / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.9
Details: 17% PEG 4000, 0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9724 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2005
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 52294 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / Num. unique all: 5047 / % possible all: 97.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
MXSYSTEMdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1V57

1v57


Resolution: 1.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 5078 9.8 %RANDOM
Rwork0.197 ---
all-51914 --
obs-50386 97.1 %-
Solvent computationBsol: 62.486 Å2
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å24.04 Å2
2--0.43 Å20 Å2
3----1.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 25 356 4009
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.21.5
X-RAY DIFFRACTIONc_bond_d0.0052
X-RAY DIFFRACTIONc_dihedral_angle_d22.82
X-RAY DIFFRACTIONc_improper_angle_d0.842.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.273 775 -
Rwork0.246 --
obs-7110 91.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3so4.par

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