[English] 日本語
Yorodumi
- PDB-7d9l: Crystal structure of E. coli Grx2: Enzyme inhibited state in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d9l
TitleCrystal structure of E. coli Grx2: Enzyme inhibited state in complex with Zinc and glutathione sulfinic acid
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / E. coli / GRX2 / Zinc / Glutathione sulfinic acid / Enzyme inhibition
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
L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE / OXYGEN MOLECULE / Glutaredoxin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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
Citation
Journal: To Be Published
Title: Crystal structure of E. coli Grx2: Enzyme inhibited state in complex with Zinc and glutathione sulfinic acid
Authors: Sreekumar, S.N. / Arockiasamy, A.
#1: Journal: J Mol Biol / Year: 2001
Title: Solution structure of Escherichia coli glutaredoxin-2 shows similarity to mammalian glutathione-S-transferases.
Authors: Xia, B. / Vlamis-Gardikas, A. / Holmgren, A. / Wright, P.E. / Dyson, H.J.
History
DepositionOct 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0177
Polymers24,3831
Non-polymers6346
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-20 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.095, 106.758, 42.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 1 molecules A

#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) / Gene: grxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TEC2

-
Non-polymers , 6 types, 162 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GSF / L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE / GLUTATHIONE SULFINATE


Mass: 339.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O8S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.81 % / Description: 2D plates.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, 20 mM GSH, 10 mM DHA 0.01M Zinc sulfate heptahydrate, 0.1M MES monohydrate pH6.5, 25%v/v Polyethylene glycol monomethyl ether 550, Protein and ...Details: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, 20 mM GSH, 10 mM DHA 0.01M Zinc sulfate heptahydrate, 0.1M MES monohydrate pH6.5, 25%v/v Polyethylene glycol monomethyl ether 550, Protein and reservoir mixed in 1:1, 1:2 and 2:1 ratio, set up using MRC Swissci 3 well plates with drop size 150 nl.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.6→42.35 Å / Num. obs: 28045 / % possible obs: 99.3 % / Redundancy: 6.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.082 / Rrim(I) all: 0.208 / Net I/σ(I): 11.7
Reflection shellResolution: 1.6→1.628 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.207 / Num. unique obs: 1401 / CC1/2: 0.555 / Rpim(I) all: 0.525 / Rrim(I) all: 1.32 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSJan 31, 2020 (BUILT 20200131)data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KX4

4kx4


Resolution: 1.61→42.319 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.591 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1823 1385 5 %RANDOM
Rwork0.1303 ---
obs0.1329 26365 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.55 Å2 / Biso mean: 13.839 Å2 / Biso min: 5.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0 Å20 Å2
2--0.37 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.61→42.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 32 156 1866
Biso mean--19.28 27.22 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131759
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171665
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.6572380
X-RAY DIFFRACTIONr_angle_other_deg1.5891.5923866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1523.29179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97815306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.627158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021930
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02336
X-RAY DIFFRACTIONr_rigid_bond_restr2.95833421
LS refinement shellResolution: 1.61→1.648 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.32 104 -
Rwork0.196 1927 -
obs--99.9 %

+
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