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- PDB-2zup: Updated crystal structure of DsbB-DsbA complex from E. coli -

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Basic information

Entry
Database: PDB / ID: 2zup
TitleUpdated crystal structure of DsbB-DsbA complex from E. coli
Components
  • Disulfide bond formation protein B
  • Thiol:disulfide interchange protein dsbA
KeywordsOXIDOREDUCTASE / disulfide bond / membrane protein / E. coli / Periplasm / Redox-active center / Cell inner membrane / Cell membrane / Chaperone / Electron transport / Membrane / Transmembrane / Transport
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor / cellular response to antibiotic / protein disulfide isomerase activity / ubiquinone binding / protein-disulfide reductase activity / protein folding / outer membrane-bounded periplasmic space / response to heat / electron transfer activity / plasma membrane
Similarity search - Function
Bromodomain-like / DsbB-like / Disulphide bond formation protein DsbB/BdbC / Disulphide bond formation protein DsbB / DsbB-like superfamily / : / Disulfide bond formation protein DsbB / Thiol:disulphide interchange protein DsbA/DsbL / : / DSBA-like thioredoxin domain ...Bromodomain-like / DsbB-like / Disulphide bond formation protein DsbB/BdbC / Disulphide bond formation protein DsbB / DsbB-like superfamily / : / Disulfide bond formation protein DsbB / Thiol:disulphide interchange protein DsbA/DsbL / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
UBIQUINONE-1 / Disulfide bond formation protein B / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.7 Å
AuthorsInaba, K. / Suzuki, M. / Murakami, S. / Nakagawa, A.
CitationJournal: Embo J. / Year: 2009
Title: Dynamic nature of disulphide bond formation catalysts revealed by crystal structures of DsbB
Authors: Inaba, K. / Murakami, S. / Nakagawa, A. / Iida, H. / Kinjo, M. / Ito, K. / Suzuki, M.
History
DepositionOct 28, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 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 dsbA
B: Disulfide bond formation protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5464
Polymers41,2302
Non-polymers3162
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-18 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.500, 165.500, 65.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-190-

ZN

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Components

#1: Protein Thiol:disulfide interchange protein dsbA / DsbA


Mass: 21122.959 Da / Num. of mol.: 1 / Mutation: C33A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pQE / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: P0AEG4, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor
#2: Protein Disulfide bond formation protein B / DsbB / Disulfide oxidoreductase


Mass: 20106.982 Da / Num. of mol.: 1 / Mutation: C8A,C49V,C130S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pQE / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: P0A6M2, Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18O4
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: 5.474029 Å3/Da / Density % sol: 77.530258 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: 23% Jeffamine ED2001, 80mM HEPES, 14.4% glycerol, 2mM ZnCl2, pH 7.0, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Sep 22, 2005
RadiationMonochromator: SI(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.7→61.2 Å / Num. obs: 10179 / % possible obs: 99.94 % / Observed criterion σ(I): -4 / Redundancy: 6.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.7
Reflection shellResolution: 3.7→3.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1450 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0044refinement
MACSCIENCEdata collection
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR
Starting model: 2HI7

2hi7


Resolution: 3.7→20 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.928 / SU B: 47.802 / SU ML: 0.688 / Cross valid method: THROUGHOUT / ESU R Free: 0.662 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33397 488 4.8 %RANDOM
Rwork0.30368 ---
obs0.30513 9622 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 205.362 Å2
Baniso -1Baniso -2Baniso -3
1-10.54 Å20 Å20 Å2
2--10.54 Å20 Å2
3----21.07 Å2
Refinement stepCycle: LAST / Resolution: 3.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 0 19 0 2661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222734
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9593722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5895330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.75424.522115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.75215444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.554157
X-RAY DIFFRACTIONr_chiral_restr0.0960.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212055
X-RAY DIFFRACTIONr_mcbond_it0.6721.51659
X-RAY DIFFRACTIONr_mcangle_it1.22822675
X-RAY DIFFRACTIONr_scbond_it0.81831075
X-RAY DIFFRACTIONr_scangle_it1.4754.51047
LS refinement shellResolution: 3.7→4.039 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.507 125 -
Rwork0.398 2181 -
obs--99.87 %

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