[English] 日本語
Yorodumi
- PDB-7p50: GlnK2 from Methanothermococcus thermolithotrophicus in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p50
TitleGlnK2 from Methanothermococcus thermolithotrophicus in complex with Mg-ATP and 2-oxoglutarate at a resolution of 1.16 A
ComponentsGlnK2 from Methanothermococcus thermolithotrophicus
KeywordsSIGNALING PROTEIN / PII-family / Methanococcales / methanogenic archaea / thermophile / hydrogenotrophic / protein regulation / inhibitor / conformational change / ATP / 2-oxoglutarate / T-loop
Function / homology2-OXOGLUTARIC ACID / ADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsMueller, M.-C. / Wagner, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Int J Mol Sci / Year: 2021
Title: The Oxoglutarate Binding Site and Regulatory Mechanism Are Conserved in Ammonium Transporter Inhibitors GlnKs from Methanococcales .
Authors: Muller, M.C. / Wagner, T.
History
DepositionJul 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GlnK2 from Methanothermococcus thermolithotrophicus
B: GlnK2 from Methanothermococcus thermolithotrophicus
C: GlnK2 from Methanothermococcus thermolithotrophicus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,54315
Polymers44,1873
Non-polymers2,35612
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12080 Å2
ΔGint-72 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.238, 58.238, 229.304
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein GlnK2 from Methanothermococcus thermolithotrophicus


Mass: 14729.015 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: GlnK2 was expressed with a His-tag in the N-terminus.
Source: (gene. exp.) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Tissue: / / Cell: / / Cell line: / / Gene: glnk2 / Organ: / / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 7 types, 526 molecules

#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.24 % / Description: Transparent spike
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MtGlnK2 was crystallized at a concentration of 30 mg/ml in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol and 500 mM NaCl. The protein was co-crystallized with 2 mM ATP, 2 mM 2- ...Details: MtGlnK2 was crystallized at a concentration of 30 mg/ml in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol and 500 mM NaCl. The protein was co-crystallized with 2 mM ATP, 2 mM 2-oxoglutarate and 2 mM MgCl2 on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). Drop of 0.6 ul of protein sample was mixed with 0.6 ul of the crystallization solution. The reservoir contained 90 ul of the following crystallization solution: 25 w/v Pentaerythritol ethoxylate (3/4 EO/OH), 100 mM MES pH 6.5.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99985 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 1.157→57.33 Å / Num. obs: 108153 / % possible obs: 93.2 % / Redundancy: 21.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.01 / Rrim(I) all: 0.05 / Net I/σ(I): 29.1
Reflection shellResolution: 1.157→1.259 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5406 / CC1/2: 0.774 / Rpim(I) all: 0.286 / Rrim(I) all: 0.709 / % possible all: 51.7

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J9D

2j9d


Resolution: 1.16→57.33 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.38 / Stereochemistry target values: ML
Details: The last steps of the refinement were performed with hydrogens in a riding mode and all atoms were considered anisotropic
RfactorNum. reflection% reflection
Rfree0.1366 5309 4.91 %
Rwork0.1168 102844 -
obs0.1178 108153 77.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.74 Å2 / Biso mean: 20.8654 Å2 / Biso min: 8.14 Å2
Refinement stepCycle: final / Resolution: 1.16→57.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 145 516 3409
Biso mean--15.16 34.02 -
Num. residues----351
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.16-1.170.367550.24231441493
1.17-1.180.2055230.21343623858
1.18-1.20.2891190.208957959813
1.2-1.210.2105360.201374077617
1.21-1.230.1741430.17394799022
1.23-1.250.1571510.17081157120826
1.25-1.260.2279930.17421634172738
1.26-1.280.21150.162338245354
1.28-1.30.1741440.15142943308767
1.3-1.320.18421700.14653596376682
1.32-1.350.19692570.13614105436296
1.35-1.370.16892300.12424278450898
1.37-1.40.14892120.10944337454999
1.4-1.430.14912120.098343844596100
1.43-1.460.1382360.095143804616100
1.46-1.490.12512350.090943364571100
1.49-1.530.12662260.09243854611100
1.53-1.570.11112400.090643724612100
1.57-1.610.11912340.089943724606100
1.61-1.670.11962260.094644064632100
1.67-1.730.12212480.099143774625100
1.73-1.80.14322290.107944024631100
1.8-1.880.13132120.106244634675100
1.88-1.980.11412330.096243874620100
1.98-2.10.12052280.09544664694100
2.1-2.260.12352130.097744614674100
2.26-2.490.13842180.111645154733100
2.49-2.850.12882270.116845264753100
2.85-3.590.14322460.128845924838100
3.59-57.330.14262480.143348605108100

+
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