[English] 日本語
Yorodumi
- PDB-6q6v: Crystal structure (trigonal form) of C36S mutant of thioredoxin h... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q6v
TitleCrystal structure (trigonal form) of C36S mutant of thioredoxin h1 from Chlamydomonas reinhardtii
ComponentsThioredoxin H-type
KeywordsELECTRON TRANSPORT / alpha/beta protein / thioredoxin fold / disulphide oxidoreductase / cell redox homeostatis
Function / homology
Function and homology information


protein-disulfide reductase activity / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Thioredoxin H-type
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsFermani, S. / Zaffagnini, M. / Lemaire, S.D.
Funding support Italy, 1items
OrganizationGrant numberCountry
FARB2012-University of Bologna Italy
CitationJournal: Antioxidants (Basel) / Year: 2019
Title: Structural and Biochemical Insights into the Reactivity of Thioredoxin h1 fromChlamydomonas reinhardtii.
Authors: Marchand, C.H. / Fermani, S. / Rossi, J. / Gurrieri, L. / Tedesco, D. / Henri, J. / Sparla, F. / Trost, P. / Lemaire, S.D. / Zaffagnini, M.
History
DepositionDec 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin H-type
B: Thioredoxin H-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7913
Polymers23,6852
Non-polymers1061
Water6,233346
1
A: Thioredoxin H-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9492
Polymers11,8431
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin H-type


Theoretical massNumber of molelcules
Total (without water)11,8431
Polymers11,8431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.742, 48.742, 143.187
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Thioredoxin H-type / Trx-H / Thioredoxin-CH1


Mass: 11842.665 Da / Num. of mol.: 2 / Mutation: C36S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: TRXH / Organ: cytoplasm / Production host: Escherichia coli (E. coli) / References: UniProt: P80028
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% (w/v) PEG 8K, 10% (w/v) PEG 10K, 0.1 M HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 8, 2014 / Details: Silicon toroidal mirror coated with Rhodium
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→42.21 Å / Num. obs: 59565 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 12.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Net I/σ(I): 14.7
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.108 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2934 / CC1/2: 0.635 / Rpim(I) all: 0.507 / Rrim(I) all: 1.311 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EP7

1ep7


Resolution: 1.22→42.21 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 20
RfactorNum. reflection% reflection
Rfree0.1743 5738 5.09 %
Rwork0.1682 --
obs0.1685 59506 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.2 Å2
Refinement stepCycle: LAST / Resolution: 1.22→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 7 346 2001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071710
X-RAY DIFFRACTIONf_angle_d1.0792325
X-RAY DIFFRACTIONf_dihedral_angle_d15.727605
X-RAY DIFFRACTIONf_chiral_restr0.085276
X-RAY DIFFRACTIONf_plane_restr0.007292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.23390.27711400.29663457X-RAY DIFFRACTION98
1.2339-1.24840.30122080.29043534X-RAY DIFFRACTION98
1.2484-1.26360.30141420.2933571X-RAY DIFFRACTION98
1.2636-1.27960.31482060.28543542X-RAY DIFFRACTION99
1.2796-1.29640.25771840.2663512X-RAY DIFFRACTION99
1.2964-1.31420.28971900.26443573X-RAY DIFFRACTION99
1.3142-1.3330.26112330.26093495X-RAY DIFFRACTION99
1.333-1.35290.27272210.2573571X-RAY DIFFRACTION99
1.3529-1.3740.27511260.24113600X-RAY DIFFRACTION99
1.374-1.39660.23861640.23053627X-RAY DIFFRACTION100
1.3966-1.42060.24361820.22093523X-RAY DIFFRACTION100
1.4206-1.44650.20961990.20563578X-RAY DIFFRACTION99
1.4465-1.47430.20851720.21213615X-RAY DIFFRACTION100
1.4743-1.50440.2061960.19853559X-RAY DIFFRACTION100
1.5044-1.53710.22741800.18983587X-RAY DIFFRACTION100
1.5371-1.57290.18151750.18313642X-RAY DIFFRACTION100
1.5729-1.61220.19031780.17913533X-RAY DIFFRACTION100
1.6122-1.65580.19811700.16893606X-RAY DIFFRACTION100
1.6558-1.70450.20671600.16753606X-RAY DIFFRACTION100
1.7045-1.75950.19122160.16473549X-RAY DIFFRACTION100
1.7595-1.82240.18052100.16363546X-RAY DIFFRACTION100
1.8224-1.89540.14181880.16273607X-RAY DIFFRACTION100
1.8954-1.98160.17931840.15193581X-RAY DIFFRACTION100
1.9816-2.08610.14272020.14723583X-RAY DIFFRACTION100
2.0861-2.21680.17291900.14563626X-RAY DIFFRACTION100
2.2168-2.3880.14422580.13813468X-RAY DIFFRACTION100
2.388-2.62820.15812250.14713552X-RAY DIFFRACTION100
2.6282-3.00840.17042180.15133581X-RAY DIFFRACTION100
3.0084-3.790.14492060.14553570X-RAY DIFFRACTION100
3.79-42.2370.14552150.14663548X-RAY DIFFRACTION100

+
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