[English] 日本語
Yorodumi
- PDB-8ool: Glutamine synthetase from Methanothermococcus thermolithotrophicu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ool
TitleGlutamine synthetase from Methanothermococcus thermolithotrophicus with TbXo4 at a resolution of 1.65 A
ComponentsGlutamine synthetase from Methanothermococcus thermolithotrophicus
KeywordsLIGASE / Nitrogen-assimilation / methanogenic archaea / allosteric activation / hydrogenotrophic / thermophile / marine / crystallophore / glutamate / ATP
Function / homologyTERBIUM(III) ION
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMueller, M.-C. / Wagner, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Societyna Germany
German Research Foundation (DFG)KU 3768/1-1 Germany
CitationJournal: Commun Biol / Year: 2024
Title: Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations.
Authors: Muller, M.C. / Lemaire, O.N. / Kurth, J.M. / Welte, C.U. / Wagner, T.
History
DepositionApr 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamine synthetase from Methanothermococcus thermolithotrophicus
B: Glutamine synthetase from Methanothermococcus thermolithotrophicus
C: Glutamine synthetase from Methanothermococcus thermolithotrophicus
D: Glutamine synthetase from Methanothermococcus thermolithotrophicus
E: Glutamine synthetase from Methanothermococcus thermolithotrophicus
F: Glutamine synthetase from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,59658
Polymers301,7766
Non-polymers7,82052
Water52,8202932
1
A: Glutamine synthetase from Methanothermococcus thermolithotrophicus
B: Glutamine synthetase from Methanothermococcus thermolithotrophicus
C: Glutamine synthetase from Methanothermococcus thermolithotrophicus
D: Glutamine synthetase from Methanothermococcus thermolithotrophicus
E: Glutamine synthetase from Methanothermococcus thermolithotrophicus
F: Glutamine synthetase from Methanothermococcus thermolithotrophicus
hetero molecules

A: Glutamine synthetase from Methanothermococcus thermolithotrophicus
B: Glutamine synthetase from Methanothermococcus thermolithotrophicus
C: Glutamine synthetase from Methanothermococcus thermolithotrophicus
D: Glutamine synthetase from Methanothermococcus thermolithotrophicus
E: Glutamine synthetase from Methanothermococcus thermolithotrophicus
F: Glutamine synthetase from Methanothermococcus thermolithotrophicus
hetero molecules


  • defined by author
  • Evidence: native gel electrophoresis, gel filtration
  • 619 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)619,193116
Polymers603,55212
Non-polymers15,640104
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area68300 Å2
ΔGint-811 kcal/mol
Surface area203520 Å2
Unit cell
Length a, b, c (Å)131.434, 228.448, 204.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-998-

HOH

21D-976-

HOH

-
Components

#1: Protein
Glutamine synthetase from Methanothermococcus thermolithotrophicus


Mass: 50296.039 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 2095 / Tissue: / / References: glutamine synthetase
#2: Chemical...
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: Tb / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2932 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.8 % / Description: Hexagonal plate
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystallization was performed in an anoxic tent (with a gas phase of 95% N2/5% H2) on a 96-well two-drop MRC crystallization plate in polystyrene (Molecular Dimensions, Suffolk, UK). The ...Details: Crystallization was performed in an anoxic tent (with a gas phase of 95% N2/5% H2) on a 96-well two-drop MRC crystallization plate in polystyrene (Molecular Dimensions, Suffolk, UK). The sitting drops contained a mix of 0.7 ml of the glutamine synthetase at 15 mg/ml with 10 mM TbXo4 and 0.7 ml of precipitant solution (35 % Pentaerythritol ethoxylate (15/4 EO/OH), 200 mM Ammonium sulphate, 100 mM HEPES pH 7.5).
PH range: /

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.65→49.78 Å / Num. obs: 361584 / % possible obs: 98.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.039 / Rrim(I) all: 0.074 / Net I/σ(I): 11.9
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.918 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 51999 / CC1/2: 0.782 / Rpim(I) all: 0.566 / Rrim(I) all: 1.081 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→49.78 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.98 / Stereochemistry target values: ML
Details: Refinement was performed with PHENIX in combination with fast automatic visual model building in COOT. Refinement was performed with considering all atoms except water anisotropic. ...Details: Refinement was performed with PHENIX in combination with fast automatic visual model building in COOT. Refinement was performed with considering all atoms except water anisotropic. Additionally, riding hydrogens were added during the refinement.
RfactorNum. reflection% reflection
Rfree0.185 17860 4.95 %
Rwork0.163 --
obs0.1641 361148 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.52 Å2
Refinement stepCycle: LAST / Resolution: 1.65→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21204 0 81 2932 24217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221915
X-RAY DIFFRACTIONf_angle_d1.48529730
X-RAY DIFFRACTIONf_dihedral_angle_d21.6788147
X-RAY DIFFRACTIONf_chiral_restr0.1173184
X-RAY DIFFRACTIONf_plane_restr0.0083922
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.36465530.331211259X-RAY DIFFRACTION97
1.67-1.690.31926280.290911199X-RAY DIFFRACTION98
1.69-1.710.32316000.27711225X-RAY DIFFRACTION98
1.71-1.730.32365960.26411278X-RAY DIFFRACTION98
1.73-1.750.2926470.246711252X-RAY DIFFRACTION98
1.75-1.780.26525220.230711347X-RAY DIFFRACTION98
1.78-1.80.26555180.209911428X-RAY DIFFRACTION98
1.8-1.830.24085200.192211365X-RAY DIFFRACTION98
1.83-1.860.22675560.172411338X-RAY DIFFRACTION98
1.86-1.890.20876800.173511253X-RAY DIFFRACTION98
1.89-1.920.22116360.17111274X-RAY DIFFRACTION98
1.92-1.960.21665480.164611419X-RAY DIFFRACTION99
1.96-1.990.19326160.166811389X-RAY DIFFRACTION99
1.99-2.030.22085580.171511380X-RAY DIFFRACTION99
2.03-2.080.21836140.17311360X-RAY DIFFRACTION99
2.08-2.130.20255940.16111481X-RAY DIFFRACTION99
2.13-2.180.17836740.147111287X-RAY DIFFRACTION99
2.18-2.240.17916260.138111451X-RAY DIFFRACTION99
2.24-2.310.17745990.13511448X-RAY DIFFRACTION99
2.31-2.380.15785890.12811468X-RAY DIFFRACTION99
2.38-2.460.16345000.139411562X-RAY DIFFRACTION99
2.46-2.560.16466890.142211453X-RAY DIFFRACTION99
2.56-2.680.17355850.150311547X-RAY DIFFRACTION99
2.68-2.820.17145740.144811552X-RAY DIFFRACTION99
2.82-30.18626500.150411569X-RAY DIFFRACTION100
3-3.230.1735980.153411586X-RAY DIFFRACTION100
3.23-3.550.14916070.153711653X-RAY DIFFRACTION100
3.55-4.070.14425440.147811750X-RAY DIFFRACTION100
4.07-5.120.15026690.141611689X-RAY DIFFRACTION100
5.13-49.780.23135700.207512026X-RAY DIFFRACTION99

+
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