[English] 日本語
Yorodumi
- PDB-1v57: Crystal Structure of the Disulfide Bond Isomerase DsbG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1v57
TitleCrystal Structure of the Disulfide Bond Isomerase DsbG
ComponentsThiol:disulfide interchange protein dsbG
KeywordsISOMERASE / oxidized dsbg / redox protein / protein disulfide isomerase / thioredoxin fold / strained redox-active center
Function / homology
Function and homology information


protein disulfide isomerase activity / : / outer membrane-bounded periplasmic space / protein homodimerization activity
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #150 / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase, DsbC/G / Disulfide bond isomerase protein N-terminal domain / : / Thioredoxin-like domain / Thioredoxin-like fold / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #150 / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase, DsbC/G / Disulfide bond isomerase protein N-terminal domain / : / Thioredoxin-like domain / Thioredoxin-like fold / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Nuclear Transport Factor 2; Chain: A, / Helix non-globular / Special / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2 Å
AuthorsHeras, B. / Edeling, M.A. / Schirra, H.J. / Raina, S. / Martin, J.L.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structures of the DsbG disulfide isomerase reveal an unstable disulfide
Authors: Heras, B. / Edeling, M.A. / Schirra, H.J. / Raina, S. / Martin, J.L.
#1: Journal: Structure / Year: 2003
Title: Dehydration converts DsbG crystal diffraction from low to high resolution.
Authors: Heras, B. / Edeling, M.A. / Byriel, K.A. / Jones, A. / Raina, S. / Martin, J.L.
History
DepositionNov 21, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thiol:disulfide interchange protein dsbG
B: Thiol:disulfide interchange protein dsbG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4806
Polymers54,0962
Non-polymers3844
Water9,152508
1
A: Thiol:disulfide interchange protein dsbG
hetero molecules

A: Thiol:disulfide interchange protein dsbG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4806
Polymers54,0962
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
2
B: Thiol:disulfide interchange protein dsbG
hetero molecules

B: Thiol:disulfide interchange protein dsbG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4806
Polymers54,0962
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)116.518, 57.047, 85.417
Angle α, β, γ (deg.)90.00, 95.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1352-

HOH

DetailsThe biological assembly is a homodimer generated from one momomer in the asymmetric unit by the operations: -x, y, -z.

-
Components

#1: Protein Thiol:disulfide interchange protein dsbG / DsbG disulfide bond isomerase


Mass: 27047.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dsbG / Plasmid: pET42b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P77202
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.75
Details: 20% PEG 4000, 0.1M sodium citrate, 0.2M ammonium sulfate, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 6, 2001 / Details: OSMIC MAXFLUX CONFOCAL BLUE
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→32.17 Å / Num. obs: 36303 / % possible obs: 95.5 % / Observed criterion σ(F): 5 / Redundancy: 3.2 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 6.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.87 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3323 / % possible all: 88

-
Processing

Software
NameVersionClassification
CRYSTALCLEAR 1.3data collection
CRYSTALCLEAR 1.3data reduction
CNSrefinement
CrystalClearV. 1.3 (MSC/RIGAKU)data reduction
CrystalClearV. 1.3 (MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: Structure of Reduced DsbG

Resolution: 2→32.17 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Refinement: maximum likelihood in CNS. Last minimisation step performed using a reduced weighting for the disulfide bond length.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3621 -RANDOM
Rwork0.2 ---
all-38006 --
obs-36299 95.4 %-
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å22.72 Å2
2--0.48 Å20 Å2
3----1.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2→32.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 20 509 4328
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.315 478 -
Rwork0.292 --
obs-4401 77.6 %

+
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