[English] 日本語
Yorodumi
- PDB-5g2z: Crystallographic structure of mutant W31A of thioredoxin from Lit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g2z
TitleCrystallographic structure of mutant W31A of thioredoxin from Litopenaeus vannamei
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE / THIOREDOXIN / SHRIMP / LITOPENAEUS VANNAMEI / MUTANT / DISULFIDE BOND
Function / homology
Function and homology information


protein-disulfide reductase activity / metal ion binding / cytosol
Similarity search - Function
Thioredoxin / 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
Biological speciesLITOPENAEUS VANNAMEI (Pacific white shrimp)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsCampos-Acevedo, A.A. / Rudino-Pinera, E.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Is dimerization a common feature in thioredoxins? The case of thioredoxin from Litopenaeus vannamei.
Authors: Campos-Acevedo, A.A. / Sotelo-Mundo, R.R. / Perez, J. / Rudino-Pinera, E.
History
DepositionApr 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THIOREDOXIN
B: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)23,6872
Polymers23,6872
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-8 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.156, 62.675, 99.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein THIOREDOXIN /


Mass: 11843.578 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUE 11 IS A SER IN THE UNIPROT DEPOSIT B1PWB9, IN THIS STRUCTURE A PHE IS CLEARLY VISIBLE ON POSITION 11.
Source: (gene. exp.) LITOPENAEUS VANNAMEI (Pacific white shrimp)
Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: B1PWB9, thioredoxin-disulfide reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SERINE IS PRESENT IN RESIDUE 11 FROM UNIPROT DEPOSIT B1PWB9, IN OUR STRUCTURE RESIDUE 11 IS A PHENILALANINE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.78 % / Description: NONE
Crystal growpH: 7
Details: 30% (W/V) POLYETHYLENE GLYCOL 3, 000. 100 MM TRIS BASE/HYDROCHLORIC ACID PH 7.0. 200 MM NACL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU-MSC R-AXIS IV / Detector: IMAGE PLATE / Date: Nov 18, 2014 / Details: VARIMAX-HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→23.43 Å / Num. obs: 17415 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 23.21 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.6
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZZX

3zzx


Resolution: 1.88→23.429 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 1738 10 %
Rwork0.1842 --
obs0.1895 17375 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.26 Å2
Refinement stepCycle: LAST / Resolution: 1.88→23.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 0 140 1788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071693
X-RAY DIFFRACTIONf_angle_d0.8382283
X-RAY DIFFRACTIONf_dihedral_angle_d15.9411067
X-RAY DIFFRACTIONf_chiral_restr0.055259
X-RAY DIFFRACTIONf_plane_restr0.005300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.93530.26411420.20091281X-RAY DIFFRACTION100
1.9353-1.99780.27861420.19591281X-RAY DIFFRACTION100
1.9978-2.06910.28861470.20431317X-RAY DIFFRACTION100
2.0691-2.15190.2351390.1921254X-RAY DIFFRACTION100
2.1519-2.24980.2511430.18721283X-RAY DIFFRACTION99
2.2498-2.36830.22671460.18031314X-RAY DIFFRACTION99
2.3683-2.51650.2451420.1971274X-RAY DIFFRACTION99
2.5165-2.71060.27521450.20071309X-RAY DIFFRACTION99
2.7106-2.98280.28741450.19831307X-RAY DIFFRACTION100
2.9828-3.41330.21841460.19631316X-RAY DIFFRACTION99
3.4133-4.29610.2331460.15631314X-RAY DIFFRACTION98
4.2961-23.43060.19151550.17571387X-RAY DIFFRACTION97

+
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