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- PDB-1jzd: DsbC-DsbDalpha complex -

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Basic information

Entry
Database: PDB / ID: 1jzd
TitleDsbC-DsbDalpha complex
Components
  • thiol:disulfide interchange protein dsbc
  • thiol:disulfide interchange protein dsbd
KeywordsOXIDOREDUCTASE / THIOL DISULFIDE OXIDOREDUCTASE / REACTION INTERMEDIATE / PROTEIN-PROTEIN COMPLEX
Function / homology
Function and homology information


protein-disulfide reductase / protein-disulfide reductase (NAD(P)H) activity / cytochrome complex assembly / response to copper ion / protein disulfide isomerase activity / protein-disulfide reductase activity / chaperone-mediated protein folding / cell redox homeostasis / outer membrane-bounded periplasmic space / periplasmic space ...protein-disulfide reductase / protein-disulfide reductase (NAD(P)H) activity / cytochrome complex assembly / response to copper ion / protein disulfide isomerase activity / protein-disulfide reductase activity / chaperone-mediated protein folding / cell redox homeostasis / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / protein homodimerization activity / plasma membrane
Similarity search - Function
Thiol:disulfide interchange protein DsbD, N-terminal domain / Disulphide bond isomerase, DsbC/G, N-terminal / Disulfide bond isomerase protein N-terminal domain / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / Thiol:disulphide interchange protein DsbD / DsbD gamma / Thiol:disulfide interchange protein DsbD, N-terminal domain ...Thiol:disulfide interchange protein DsbD, N-terminal domain / Disulphide bond isomerase, DsbC/G, N-terminal / Disulfide bond isomerase protein N-terminal domain / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / Thiol:disulphide interchange protein DsbD / DsbD gamma / Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal / Cytochrome C biogenesis protein, transmembrane domain / Cytochrome C biogenesis protein transmembrane region / 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 / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbC / Thiol:disulfide interchange protein DsbC / Thiol:disulfide interchange protein DsbD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 15, 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: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: thiol:disulfide interchange protein dsbc
B: thiol:disulfide interchange protein dsbc
C: thiol:disulfide interchange protein dsbd


Theoretical massNumber of molelcules
Total (without water)62,3773
Polymers62,3773
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-24 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.910, 68.910, 230.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein thiol:disulfide interchange protein dsbc


Mass: 23802.355 Da / Num. of mol.: 2 / Fragment: DsbC + N-terminal 4 residues from His-tag / 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: Protein thiol:disulfide interchange protein dsbd / C-type cytochrome biogenesis protein cycZ / inner membrane copper tolerance protein


Mass: 14772.376 Da / Num. of mol.: 1 / Fragment: DsbDalpha / Mutation: C103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dsbD / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha Z / References: UniProt: P36655
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: PEG, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
SYNCHROTRONESRF ID2910.980.98
SYNCHROTRONEMBL/DESY, HAMBURG BW7B20.830.83
ROTATING ANODERIGAKU RU30031.54181.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 9, 2001
ADSC QUANTUM 42CCDJul 4, 2001
MARRESEARCH3IMAGE PLATEMay 16, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.831
31.54181
ReflectionResolution: 1.9→30 Å / Num. all: 24849 / Num. obs: 24849 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 7.4
Reflection shellResolution: 2.3→2.44 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1eej (DsbC monomer)

1eej


Resolution: 2.3→29.77 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3047250.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1268 5 %RANDOM
Rwork0.234 ---
obs-24849 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.1893 Å2 / ksol: 0.365134 e/Å3
Displacement parametersBiso mean: 43.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å20 Å2
2--1.47 Å20 Å2
3----2.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 0 124 4347
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.672
X-RAY DIFFRACTIONc_scbond_it2.282
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 216 5.3 %
Rwork0.282 3825 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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