[English] 日本語
Yorodumi
- PDB-5gl3: Crystal structure of TON_0340 in complex with Mg -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gl3
TitleCrystal structure of TON_0340 in complex with Mg
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
D-glutamate cyclase-like C-terminal domain-containing protein
Similarity search - Component
Biological speciesThermococcus onnurineus NA1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.1Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,93718
Polymers174,6456
Non-polymers29212
Water3,783210
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3126
Polymers58,2152
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3126
Polymers58,2152
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Uncharacterized protein
E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3126
Polymers58,2152
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.982, 106.982, 363.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein
Uncharacterized protein


Mass: 29107.531 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus NA1 (archaea) / Strain: NA1 / Gene: TON_0340 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YTD8
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: sodium acetate pH, 16% 2-methyl-2,4-pentanediol,magnesium acetate

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 73586 / % possible obs: 87.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.061 / Χ2: 2.114 / Net I/av σ(I): 31.136 / Net I/σ(I): 16.2 / Num. measured all: 423552
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.442.50.20326610.91264.4
2.44-2.492.70.19928010.96668.1
2.49-2.532.90.18828811.02770.8
2.53-2.5930.17230731.02674.7
2.59-2.643.20.16631981.09377.4
2.64-2.73.50.15932691.13379.2
2.7-2.773.80.14734681.23784.2
2.77-2.854.10.13735461.34885.6
2.85-2.934.50.12636101.44787.4
2.93-3.0250.11537691.58690.5
3.02-3.135.40.10838621.79392.8
3.13-3.265.90.139231.9894.4
3.26-3.416.50.0940052.27196
3.41-3.587.20.0840842.50797.3
3.58-3.817.60.07340942.58497.6
3.81-4.180.06641502.5798.2
4.1-4.528.50.0641712.7198.7
4.52-5.178.50.05542072.54698.6
5.17-6.517.90.04842731.92898.2
6.51-508.60.03345412.49498

-
Processing

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

4fc5


Resolution: 2.4→50 Å / Cross valid method: FREE R-VALUE / σ(F): 30
RfactorNum. reflection% reflection
Rfree0.243 3738 4.5 %
Rwork0.199 69784 -
obs-73552 87.8 %
Solvent computationBsol: 28.9921 Å2
Displacement parametersBiso max: 100.91 Å2 / Biso mean: 43.3875 Å2 / Biso min: 15.67 Å2
Baniso -1Baniso -2Baniso -3
1--2.308 Å20 Å20 Å2
2---2.308 Å20 Å2
3---4.617 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12196 0 12 210 12418
Biso mean--47.32 37.11 -
Num. residues----1604
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2631.5
X-RAY DIFFRACTIONc_scbond_it2.0212
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scangle_it3.0282.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param

+
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