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- PDB-1jzo: DsbC C101S -

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Basic information

Entry
Database: PDB / ID: 1jzo
TitleDsbC C101S
ComponentsTHIOL:DISULFIDE INTERCHANGE PROTEIN DSBC
KeywordsOXIDOREDUCTASE / disulfide bond isomerase / thiol oxidoreductase / DsbC / thioredoxin fold
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 / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase, DsbC/G / Disulfide bond isomerase protein N-terminal domain / : / Thioredoxin-like domain / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. ...Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase, DsbC/G / Disulfide bond isomerase protein N-terminal domain / : / Thioredoxin-like domain / Thioredoxin-like fold / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Nuclear Transport Factor 2; Chain: A, / Thioredoxin domain / 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: 1.92 Å
AuthorsHaebel, P.W. / Goldstone, D. / Katzen, F. / Beckwith, J. / Metcalf, P.
CitationJournal: Embo J. / Year: 2002
Title: The Disulfide Bond Isomerase DsbC is Activated by an Immunoglobulin-fold Thiol Oxidoreductase: Crystal Structure of the DsbC-DsbDalpha complex.
Authors: Haebel, P.W. / Goldstone, D. / Katzen, F. / Beckwith, J. / Metcalf, P.
History
DepositionSep 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBC
B: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBC


Theoretical massNumber of molelcules
Total (without water)46,9442
Polymers46,9442
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-15 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.400, 78.294, 95.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein THIOL:DISULFIDE INTERCHANGE PROTEIN DSBC


Mass: 23471.949 Da / Num. of mol.: 2 / Fragment: DsbC / Mutation: C101S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dsbC / Plasmid: pProEX HT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P21892, UniProt: P0AEG6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 48.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG550 MME, TRIS, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 13, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 34245 / Num. obs: 34245 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 28.4
Reflection shellResolution: 1.9→2.02 Å / Rmerge(I) obs: 0.42 / % possible all: 95.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code: 1eej

1eej


Resolution: 1.92→32.69 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 382422.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1660 5 %RANDOM
Rwork0.22 ---
all-34245 --
obs-33417 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 88.94 Å2 / ksol: 0.412763 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.86 Å20 Å20 Å2
2--7.27 Å20 Å2
3----1.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.92→32.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 0 247 3517
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 205 4.9 %
Rwork0.253 4005 -
obs--71.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.TOP
X-RAY DIFFRACTION4ION.TOP

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