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- PDB-1uc7: Crystal structure of DsbDgamma -

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Basic information

Entry
Database: PDB / ID: 1uc7
TitleCrystal structure of DsbDgamma
ComponentsThiol:disulfide interchange protein dsbD
KeywordsOXIDOREDUCTASE / thioredoxin-fold
Function / homology
Function and homology information


protein-disulfide reductase / protein-disulfide reductase (NAD(P)H) activity / cytochrome complex assembly / cell redox homeostasis / membrane => GO:0016020 / electron transfer activity / plasma membrane
Similarity search - Function
Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / Thioredoxin-like / 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, conserved site / Thioredoxin family active site. ...Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / Thioredoxin-like / 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, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKim, J.H. / Kim, S.J. / Jeong, D.G. / Son, J.H. / Ryu, S.E.
CitationJournal: FEBS LETT. / Year: 2003
Title: Crystal structure of DsbDgamma reveals the mechanism of redox potential shift and substrate specificity(1)
Authors: Kim, J.H. / Kim, S.J. / Jeong, D.G. / Son, J.H. / Ryu, S.E.
History
DepositionApr 9, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein dsbD
B: Thiol:disulfide interchange protein dsbD


Theoretical massNumber of molelcules
Total (without water)27,9172
Polymers27,9172
Non-polymers00
Water2,126118
1
A: Thiol:disulfide interchange protein dsbD


Theoretical massNumber of molelcules
Total (without water)13,9591
Polymers13,9591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol:disulfide interchange protein dsbD


Theoretical massNumber of molelcules
Total (without water)13,9591
Polymers13,9591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.330, 57.660, 126.600
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 dsbD / DsbDgamma


Mass: 13958.721 Da / Num. of mol.: 2 / Fragment: C-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P58162, protein-disulfide reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1.89 Å3/Da / Density % sol: 34.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEK 8000, sodium acetate, ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU30011.5418
SYNCHROTRONPAL/PLS 6B20.9795, 0.9792, 0.9717
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEMay 2, 2001mirrors
MACSCIENCE2IMAGE PLATEMay 13, 2001mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1confocalSINGLE WAVELENGTHMx-ray1
2mirrorsMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97951
30.97921
40.97171
ReflectionResolution: 1.9→99 Å / Num. all: 18231 / Num. obs: 17648 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091
Reflection shellResolution: 1.9→2 Å / % possible all: 84.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→99 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.218 845 ramdom
Rwork0.185 --
all0.191 18231 -
obs0.191 17604 -
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 0 118 2090
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.15
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_dihedral_angle_d23.2

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