[English] 日本語
Yorodumi
- PDB-8pr6: Crystal structure of Corynebacterium glutamicum mycoredoxin-3 at ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pr6
TitleCrystal structure of Corynebacterium glutamicum mycoredoxin-3 at 1.7 A resolution.
ComponentsThioredoxin family protein
KeywordsOXIDOREDUCTASE / Mycoredoxin / Corynebacterium glutamicum / oxidase / swapped homodimer / redox biology
Function / homologyGlutaredoxin-like / Glutaredoxin-like domain (DUF836) / Thioredoxin-like superfamily / Glutaredoxin
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBaranova, E.V. / Wahni, K. / Ezerina, D. / Messens, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Other governmentVIB C0701JOME Belgium
CitationJournal: Redox Biochem. Chem. / Year: 2023
Title: Unveiling the enigmatic traits of Corynebacterium glutamicum mycoredoxin-3: A tiny redox protein displaying swapped homodimer formation and DsbA-like oxidase activity
Authors: Wahni, K. / Baranova, E. / Ezerina, D. / Van Molle, I. / Van Laer, K. / Messens, J.
History
DepositionJul 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Structure summary
Category: citation / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_id_ISSN

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin family protein
B: Thioredoxin family protein


Theoretical massNumber of molelcules
Total (without water)19,1152
Polymers19,1152
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-23 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.124, 36.248, 68.719
Angle α, β, γ (deg.)90.00, 99.01, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Thioredoxin family protein / Mrx3


Mass: 9557.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: AUO95_11055 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Q6BKH4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.5 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.2 M MgCl2, 0.1 M Bis-Tris (pH 5.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9195 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 1.7→33.4 Å / Num. obs: 19317 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.081 / Net I/σ(I): 9.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2791 / Rrim(I) all: 0.82 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→32.23 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.279 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25679 1004 5.2 %RANDOM
Rwork0.2172 ---
obs0.21927 18311 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.009 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20.01 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→32.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1192 0 0 105 1297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131235
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171151
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.6161688
X-RAY DIFFRACTIONr_angle_other_deg1.4021.5822663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1955.061164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.0724.0367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80215205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.344158
X-RAY DIFFRACTIONr_chiral_restr0.0830.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021537
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02235
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7042.79646
X-RAY DIFFRACTIONr_mcbond_other2.6982.788645
X-RAY DIFFRACTIONr_mcangle_it3.644.172810
X-RAY DIFFRACTIONr_mcangle_other3.6384.174811
X-RAY DIFFRACTIONr_scbond_it3.5673.167589
X-RAY DIFFRACTIONr_scbond_other3.5563.16587
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2064.598877
X-RAY DIFFRACTIONr_long_range_B_refined6.17534.511339
X-RAY DIFFRACTIONr_long_range_B_other6.14834.2181320
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 74 -
Rwork0.338 1355 -
obs--99.93 %

+
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