[English] 日本語
Yorodumi
- PDB-7dkr: Crystal structure of native E. coli Grx2 at 2.38 A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dkr
TitleCrystal structure of native E. coli Grx2 at 2.38 A
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / E. coli Grx2 / Native
Function / homology
Function and homology information


Glutaredoxin-2 / Glutaredoxin 2, C-terminal / Glutaredoxin 2, C terminal domain / Glutaredoxin active site / Glutaredoxin active site. / Glutathione S-transferase, N-terminal domain / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.378 Å
AuthorsSreekumar, S.N. / Arockiasamy, A.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR28766/BRB/10/1701/2018 India
Department of Biotechnology (DBT, India)BT/PR28080/BID/7/836/2018 India
CitationJournal: To Be Published
Title: Crystal structure of native E. coli Grx2 at 2.38 A
Authors: Sreekumar, S.N. / Arockiasamy, A.
History
DepositionNov 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutaredoxin


Theoretical massNumber of molelcules
Total (without water)24,3831
Polymers24,3831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10430 Å2
Unit cell
Length a, b, c (Å)28.470, 78.950, 89.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glutaredoxin / Glutaredoxin 2 (Grx2) / Glutaredoxin glutaredoxin / Glutaredoxin / GrxB family / Glutaredoxin-2 / ...Glutaredoxin 2 (Grx2) / Glutaredoxin glutaredoxin / Glutaredoxin / GrxB family / Glutaredoxin-2 / Glutaredoxin-2 Grx2


Mass: 24383.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TEC2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 39.9 % / Description: 2D Crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein solution: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, Reservoir condition:0.1M HEPES pH:7.5, 20% w/v PEG 10000, Protein/reservoir mixed in 1:1, 1:2 and 2:1 ratio, set up using MRC ...Details: Protein solution: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, Reservoir condition:0.1M HEPES pH:7.5, 20% w/v PEG 10000, Protein/reservoir mixed in 1:1, 1:2 and 2:1 ratio, set up using MRC Swissci 3 well plates with the drop size of 150 nl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→89.28 Å / Num. obs: 8647 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.036 / Rrim(I) all: 0.12 / Χ2: 0.92 / Net I/σ(I): 15.2
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 6.5 / Num. unique obs: 877 / CC1/2: 0.973 / Rpim(I) all: 0.106 / Rrim(I) all: 0.332 / Χ2: 0.89 / % possible all: 100

-
Processing

Software
NameVersionClassification
SCALA0.7.4data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KX4

4kx4


Resolution: 2.378→39.475 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 396 4.6 %
Rwork0.1947 8205 -
obs0.1973 8601 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.34 Å2 / Biso mean: 18.5777 Å2 / Biso min: 5.96 Å2
Refinement stepCycle: final / Resolution: 2.378→39.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 0 0 0 1712
Num. residues----215
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.378-2.72210.29921250.21612660
2.7221-3.42920.27841330.21512699

+
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