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- PDB-1vrs: Crystal structure of the disulfide-linked complex between the N-t... -

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Basic information

Entry
Database: PDB / ID: 1vrs
TitleCrystal structure of the disulfide-linked complex between the N-terminal and C-terminal domain of the electron transfer catalyst DsbD
Components(Thiol:disulfide interchange protein dsbD) x 2
KeywordsOXIDOREDUCTASE / DsbD / immunoglobulin-like / thioredoxin-like / disulfide-linked
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 reductase activity / cell redox homeostasis / electron transfer activity / plasma membrane
Similarity search - Function
Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulphide interchange protein DsbD / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / DsbD gamma / Thioredoxin-like / 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 ...Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulphide interchange protein DsbD / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / DsbD gamma / Thioredoxin-like / 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. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbD
Similarity search - Component
Biological speciesEscherichia coli str. K12 substr. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsRozhkova, A. / Stirnimann, C.U. / Frei, P. / Grauschopf, U. / Brunisholz, R. / Gruetter, M.G. / Capitani, G. / Glockshuber, R.
CitationJournal: Embo J. / Year: 2004
Title: Structural basis and kinetics of inter- and intramolecular disulfide exchange in the redox catalyst DsbD
Authors: Rozhkova, A. / Stirnimann, C.U. / Frei, P. / Grauschopf, U. / Brunisholz, R. / Gruetter, M.G. / Capitani, G. / Glockshuber, R.
History
DepositionJun 17, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionJul 12, 2005ID: 1SE1
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 20, 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 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 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 dsbD
D: Thiol:disulfide interchange protein dsbD
B: Thiol:disulfide interchange protein dsbD
E: Thiol:disulfide interchange protein dsbD
C: Thiol:disulfide interchange protein dsbD
F: Thiol:disulfide interchange protein dsbD


Theoretical massNumber of molelcules
Total (without water)93,1936
Polymers93,1936
Non-polymers00
Water5,116284
1
A: Thiol:disulfide interchange protein dsbD
D: Thiol:disulfide interchange protein dsbD


Theoretical massNumber of molelcules
Total (without water)31,0642
Polymers31,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-15 kcal/mol
Surface area12540 Å2
MethodPISA
2
B: Thiol:disulfide interchange protein dsbD
E: Thiol:disulfide interchange protein dsbD


Theoretical massNumber of molelcules
Total (without water)31,0642
Polymers31,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-16 kcal/mol
Surface area12880 Å2
MethodPISA
3
C: Thiol:disulfide interchange protein dsbD
F: Thiol:disulfide interchange protein dsbD


Theoretical massNumber of molelcules
Total (without water)31,0642
Polymers31,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-11 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.46, 52.60, 107.92
Angle α, β, γ (deg.)90.00, 100.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thiol:disulfide interchange protein dsbD / Protein-disulfide reductase / C-type cytochrome biogenesis protein cycZ / Inner membrane copper ...Protein-disulfide reductase / C-type cytochrome biogenesis protein cycZ / Inner membrane copper tolerance protein


Mass: 15982.631 Da / Num. of mol.: 3 / Fragment: N-terminal domain, Residues 1-143 / Mutation: C103S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Gene: DSBD, DIPZ, CYCZ, CUTA2, B4136 / Plasmid: pDsbA3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Rosetta / References: UniProt: P36655, protein-disulfide reductase
#2: Protein Thiol:disulfide interchange protein dsbD / Protein-disulfide reductase / C-type cytochrome biogenesis protein cycZ / Inner membrane copper ...Protein-disulfide reductase / C-type cytochrome biogenesis protein cycZ / Inner membrane copper tolerance protein


Mass: 15081.867 Da / Num. of mol.: 3 / Fragment: C-terminal domain, Residues 438-565 / Mutation: C464S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Gene: DSBD, DIPZ, CYCZ, CUTA2, B4136 / Plasmid: pDsbA3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Rosetta / References: UniProt: P36655, protein-disulfide reductase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: sodium acetate, sodium formate, PEG 2000 MME, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 98.2 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.751 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 5, 2003 / Details: Dynamically bendable mirror
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.751 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. all: 24676 / Num. obs: 24336 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 68.8 Å2 / Rsym value: 0.08 / Net I/σ(I): 16.1
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 2376 / Rsym value: 0.362 / % possible all: 97.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JZD

1jzd


Resolution: 2.85→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.284 707 RANDOM
Rwork0.224 --
all-24676 -
obs-24336 -
Displacement parametersBiso mean: 38.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.058 Å20 Å22.138 Å2
2--2.236 Å20 Å2
3---3.822 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5670 0 0 284 5954
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0076
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d25.16
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.4741.5
X-RAY DIFFRACTIONc_mcangle_it2.5032
X-RAY DIFFRACTIONc_scbond_it2.3152
X-RAY DIFFRACTIONc_scangle_it3.6432.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.043
RfactorNum. reflection
Rfree0.443 105
Rwork0.349 -
obs-3693
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param

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