[English] 日本語
Yorodumi
- PDB-2zuq: Crystal structure of DsbB-Fab complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zuq
TitleCrystal structure of DsbB-Fab complex
Components
  • Disulfide bond formation protein B
  • Fab fragment heavy chain
  • Fab fragment light chain
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 ...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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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


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


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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more