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- PDB-2zuq: Crystal structure of DsbB-Fab complex -

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Basic information

Entry
Database: PDB / ID: 2zuq
TitleCrystal structure of DsbB-Fab complex
Components
  • Disulfide bond formation protein B
  • Fab fragment heavy chainFragment antigen-binding
  • Fab fragment light chainFragment antigen-binding
KeywordsOxidoreductase/IMMUNE SYSTEM / disulfide bond / membrane protein / Fab / E. coli / Cell inner membrane / Cell membrane / Chaperone / Electron transport / Membrane / Oxidoreductase / Redox-active center / Transmembrane / Transport / Oxidoreductase-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor / ubiquinone binding / protein-disulfide reductase activity / protein folding / 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 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich ...Bromodomain-like / DsbB-like / Disulphide bond formation protein DsbB/BdbC / Disulphide bond formation protein DsbB / DsbB-like superfamily / Disulfide bond formation protein DsbB / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
UBIQUINONE-1 / Disulfide bond formation protein B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsInaba, K. / Suzuki, M. / Murakami, S.
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 1.2Nov 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 1.3Nov 1, 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

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Assembly

Deposited unit
A: Disulfide bond formation protein B
B: Fab fragment light chain
C: Fab fragment heavy chain
D: Disulfide bond formation protein B
E: Fab fragment light chain
F: Fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7768
Polymers140,2766
Non-polymers5012
Water0
1
A: Disulfide bond formation protein B
B: Fab fragment light chain
C: Fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3884
Polymers70,1383
Non-polymers2501
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Disulfide bond formation protein B
E: Fab fragment light chain
F: Fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3884
Polymers70,1383
Non-polymers2501
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)269.307, 51.480, 125.845
Angle α, β, γ (deg.)90.00, 106.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Disulfide bond formation protein B / / DsbB / Disulfide oxidoreductase


Mass: 20106.982 Da / Num. of mol.: 2 / Mutation: C8A,C41S,C49V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dsbB / Plasmid: pQE70 / 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
#2: Antibody Fab fragment light chain / Fragment antigen-binding


Mass: 26364.410 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Fab fragment is obtained by papain digestion of a selected monoclonal antibody.
Source: (natural) mus musculus (house mouse)
#3: Antibody Fab fragment heavy chain / Fragment antigen-binding


Mass: 23666.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Fab fragment is obtained by papain digestion of a selected monoclonal antibody.
Source: (natural) mus musculus (house mouse)
#4: Chemical ChemComp-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18O4

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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: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 15% PEG3350, pH 7, VAPOR DIFFUSION, 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: May 19, 2008 / Details: LH-coated mirror
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: 3.3→47.51 Å / Num. obs: 25296 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.7
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.865 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3560 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.5.0044refinement
MACSCIENCEdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IGT

1igt


Resolution: 3.3→45.64 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.844 / SU B: 39.752 / SU ML: 0.664 / Cross valid method: THROUGHOUT / ESU R Free: 0.725 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.35119 1316 5.2 %RANDOM
Rwork0.27544 ---
obs0.27949 23953 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.487 Å2
Baniso -1Baniso -2Baniso -3
1-3 Å20 Å2-1.23 Å2
2--1.36 Å20 Å2
3----5.07 Å2
Refinement stepCycle: LAST / Resolution: 3.3→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8955 0 36 0 8991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229222
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.96112561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.06851149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76623.797345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.161151477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4431536
X-RAY DIFFRACTIONr_chiral_restr0.1050.21420
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216856
X-RAY DIFFRACTIONr_mcbond_it0.4951.55778
X-RAY DIFFRACTIONr_mcangle_it0.92329343
X-RAY DIFFRACTIONr_scbond_it0.84533444
X-RAY DIFFRACTIONr_scangle_it1.5274.53218
LS refinement shellResolution: 3.303→3.388 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 95 -
Rwork0.343 1638 -
obs--93.37 %

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