[English] 日本語
Yorodumi
- PDB-7c12: beta1 domain-swapped structure of monothiol cGrx1(C16S) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c12
Titlebeta1 domain-swapped structure of monothiol cGrx1(C16S)
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / glutaredoxin-1 / Grx1 / domain-swapping
Function / homology
Function and homology information


cell redox homeostasis / electron transfer activity
Similarity search - Function
: / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAlkaliphilus oremlandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsLee, K. / Hwang, K.Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A44A1022589 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1A2C2005670 Korea, Republic Of
CitationJournal: Iucrj / Year: 2020
Title: Monothiol and dithiol glutaredoxin-1 from clostridium oremlandii: identification of domain-swapped structures by NMR, X-ray crystallography and HDX mass spectrometry.
Authors: Lee, K. / Yeo, K.J. / Choi, S.H. / Lee, E.H. / Kim, B.K. / Kim, S. / Cheong, H.-K. / Lee, W.-K. / Kim, H.-Y. / Hwang, E. / Woo, J.R. / Lee, S.-J. / Hwang, K.Y.
History
DepositionMay 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutaredoxin
B: Glutaredoxin
C: Glutaredoxin
D: Glutaredoxin


Theoretical massNumber of molelcules
Total (without water)38,6804
Polymers38,6804
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-39 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.547, 67.547, 72.616
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

-
Components

#1: Protein
Glutaredoxin


Mass: 9669.997 Da / Num. of mol.: 4 / Mutation: U13C, C16S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkaliphilus oremlandii (strain OhILAs) (bacteria)
Strain: OhILAs / Gene: Clos_2129 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8MIN3
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES pH7.5, 20% PEG 400, 8% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9065 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 51.13 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.039 / Rrim(I) all: 0.108 / Χ2: 2.502 / Net I/σ(I): 14.5 / Num. measured all: 62576
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.8540.4734480.1280.2570.5421.73698.9
2.85-2.94.30.4674290.1590.2470.5311.71799.3
2.9-2.964.60.4344670.3320.220.4891.7698.1
2.96-3.024.60.4074510.2910.2050.4581.81699.3
3.02-3.084.70.3634490.5040.180.4071.65399.1
3.08-3.155.10.344480.7150.160.3781.79399.6
3.15-3.235.70.2914450.840.130.321.83699.1
3.23-3.3260.2754750.8410.1190.3011.87599.4
3.32-3.426.40.2284650.9420.0940.2481.933100
3.42-3.5370.1724440.9770.0680.1862.05100
3.53-3.657.40.1494640.980.0560.162.264100
3.65-3.87.90.144490.9860.0510.1492.65399.1
3.8-3.977.70.1074580.9930.0390.1142.49899.6
3.97-4.188.50.0924410.9960.0320.0972.69499.8
4.18-4.448.90.0814570.9960.0270.0852.75599.8
4.44-4.798.70.0654580.9980.0220.0682.94199.6
4.79-5.279.10.0634450.9980.0210.0662.70499.8
5.27-6.0390.0694560.9980.0240.0732.97100
6.03-7.599.10.0664690.9990.0220.073.41699.8
7.59-509.20.0494470.9980.0170.0523.59398.9

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C10

7c10


Resolution: 2.803→33.773 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 2.15 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2789 895 9.88 %
Rwork0.2249 8160 -
obs0.23 9055 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.65 Å2 / Biso mean: 51.8392 Å2 / Biso min: 15.04 Å2
Refinement stepCycle: final / Resolution: 2.803→33.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 0 0 2312
Num. residues----292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.803-2.97830.34461470.2894134599
2.9783-3.20810.32021580.2623138399
3.2081-3.53070.31611420.2441350100
3.5307-4.04080.26931600.22261338100
4.0408-5.08820.26931470.1931371100
5.0882-33.7730.23721410.21221373100

+
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