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- PDB-5nhi: Crystal structure of the Escherichia coli N-terminal domain of Ds... -

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Basic information

Entry
Database: PDB / ID: 5nhi
TitleCrystal structure of the Escherichia coli N-terminal domain of DsbD (nDsbD) without the cap-loop region
ComponentsThiol:disulfide interchange protein DsbD
KeywordsOXIDOREDUCTASE / Immunoglobulin-like fold / Thiol disulfide oxidoreductase / electron transport
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 / membrane => GO:0016020 / electron transfer activity / plasma membrane
Similarity search - Function
Thiol:disulfide interchange protein DsbD, N-terminal domain / 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 ...Thiol:disulfide interchange protein DsbD, N-terminal domain / 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. / Thioredoxin domain / Thioredoxin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbD / Thiol:disulfide interchange protein DsbD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSaridakis, E. / Stelzl, L.S. / Mavridou, D.A.I. / Redfield, C.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust092532 United Kingdom
Medical Research Council (United Kingdom)MR/M009505/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the Escherichia coli N-terminal domain of DsbD (nDsbD) without the cap-loop region
Authors: Stelzl, L.S. / Mavridou, D.A.I. / Saridakis, E. / Redfield, C.
History
DepositionMar 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rrim_I_all
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)29,5912
Polymers29,5912
Non-polymers00
Water1,06359
1
A: Thiol:disulfide interchange protein DsbD


Theoretical massNumber of molelcules
Total (without water)14,7961
Polymers14,7961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiol:disulfide interchange protein DsbD


Theoretical massNumber of molelcules
Total (without water)14,7961
Polymers14,7961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.332, 81.338, 46.394
Angle α, β, γ (deg.)90.00, 100.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thiol:disulfide interchange protein DsbD / Protein-disulfide reductase / Disulfide reductase


Mass: 14795.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dsbD, EL75_4028, EL79_4206, EL80_4122 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0A0GNS2, UniProt: P36655*PLUS, protein-disulfide reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5
Details: 28% PEG 4000, 0.1M ammonium sulphate, 0.1M sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→39.771 Å / Num. obs: 9880 / % possible obs: 70.9 % / Redundancy: 1.9 % / Rpim(I) all: 0.161 / Rrim(I) all: 0.257 / Rsym value: 0.197 / Net I/σ(I): 4.6
Reflection shell
Resolution (Å)Redundancy (%)CC1/2Rpim(I) allDiffraction-ID% possible all
2.2-2.281.50.7820.343135.4
2.28-2.371.50.6840.39148.1
2.37-2.481.60.8460.351163.6
2.48-2.611.80.8260.334176.3
2.61-2.771.90.8750.289178.3
2.77-2.9920.9210.214179.9
2.99-3.2920.9230.181182.6
3.29-3.7620.9850.166181
3.76-4.741.90.9650.13181.4
4.74-39.77120.9670.106181

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PFU

3pfu


Resolution: 2.6→39.771 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.54
RfactorNum. reflection% reflection
Rfree0.2917 336 4.94 %
Rwork0.2522 --
obs0.2543 6808 80.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 0 59 1825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031829
X-RAY DIFFRACTIONf_angle_d0.7212500
X-RAY DIFFRACTIONf_dihedral_angle_d12.984656
X-RAY DIFFRACTIONf_chiral_restr0.025274
X-RAY DIFFRACTIONf_plane_restr0.004331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-3.27550.33091550.27463199X-RAY DIFFRACTION80
3.2755-39.77560.27391810.24043273X-RAY DIFFRACTION81
Refinement TLS params.Method: refined / Origin x: 11.0918 Å / Origin y: -13.1101 Å / Origin z: 8.9065 Å
111213212223313233
T0.1619 Å20.0004 Å2-0.0108 Å2-0.1379 Å2-0.0134 Å2--0.1416 Å2
L0.0411 °2-0.002 °2-0.0043 °2-0.0212 °20.0017 °2--0.0116 °2
S-0.067 Å °0.0253 Å °-0.0332 Å °0.0374 Å °0.0432 Å °0.0024 Å °-0.0062 Å °-0.0372 Å °-0.0071 Å °
Refinement TLS groupSelection details: all

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