[English] 日本語
Yorodumi
- PDB-5gkx: Crystal structure of TON_0340, apo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gkx
TitleCrystal structure of TON_0340, apo form
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / TON_0340 / Thermococcus onnurineus / Mn2+-dependent phosphatase
Function / homology
Function and homology information


D-glutamate cyclase activity / glutamate metabolic process / metal ion binding
Similarity search - Function
TON_0340 / D-glutamate cyclase-like, C-terminal / D-glutamate cyclase-like, C-terminal / inorganic pyrophosphatase (n-terminal core) / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / D-glutamate cyclase-like C-terminal domain-containing protein
Similarity search - Component
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLee, S.G. / Sohn, Y.S. / Oh, B.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Oceans and Fisheries Korea, Republic Of
Citation
Journal: PLoS ONE / Year: 2016
Title: Identification of a Highly Conserved Hypothetical Protein TON_0340 as a Probable Manganese-Dependent Phosphatase.
Authors: Sohn, Y.S. / Lee, S.G. / Lee, K.H. / Ku, B. / Shin, H.C. / Cha, S.S. / Kim, Y.G. / Lee, H.S. / Kang, S.G. / Oh, B.H.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Experimental phasing using zinc anomalous scattering.
Authors: Cha, S.S. / An, Y.J. / Jeong, C.S. / Kim, M.K. / Lee, S.G / Lee, K.H. / Oh, B.H.
History
DepositionJul 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7779
Polymers56,1132
Non-polymers6657
Water6,503361
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.574, 80.209, 85.459
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Uncharacterized protein


Mass: 28056.316 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 12-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0340 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YTD8
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate pH6.5. ammonium phosphate monobasic,

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 32203 / % possible obs: 90.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.076 / Net I/av σ(I): 14.414 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.01-2.042.60.253170.4
2.04-2.082.80.237181.4
2.08-2.122.90.233181.2
2.12-2.173.20.215183.8
2.17-2.213.40.204186
2.21-2.263.70.198189.4
2.26-2.323.70.178188.5
2.32-2.3840.168189.6
2.38-2.454.10.159188.5
2.45-2.534.30.149191.2
2.53-2.624.40.136193
2.62-2.734.60.121192.5
2.73-2.854.90.116193.3
2.85-35.20.097194.8
3-3.195.60.084195.9
3.19-3.445.80.071196.4
3.44-3.786.30.057197.3
3.78-4.336.50.045197.1
4.33-5.456.70.04196.5
5.45-506.40.036195.7

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
CNSrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FC5

4fc5


Resolution: 2.01→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.238 --
Rwork0.208 --
obs-32135 90 %
Displacement parametersBiso max: 64.79 Å2 / Biso mean: 17.6098 Å2 / Biso min: 1 Å2
Refinement stepCycle: LAST / Resolution: 2.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 35 361 4325

+
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