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Yorodumi- PDB-7p50: GlnK2 from Methanothermococcus thermolithotrophicus in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p50 | ||||||
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Title | GlnK2 from Methanothermococcus thermolithotrophicus in complex with Mg-ATP and 2-oxoglutarate at a resolution of 1.16 A | ||||||
Components | GlnK2 from Methanothermococcus thermolithotrophicus | ||||||
Keywords | SIGNALING PROTEIN / PII-family / Methanococcales / methanogenic archaea / thermophile / hydrogenotrophic / protein regulation / inhibitor / conformational change / ATP / 2-oxoglutarate / T-loop | ||||||
Function / homology | 2-OXOGLUTARIC ACID / ADENOSINE-5'-TRIPHOSPHATE Function and homology information | ||||||
Biological species | Methanothermococcus thermolithotrophicus DSM 2095 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å | ||||||
Authors | Mueller, M.-C. / Wagner, T. | ||||||
Funding support | Germany, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p50.cif.gz | 181.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p50.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7p50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p50_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 7p50_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 7p50_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 7p50_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/7p50 ftp://data.pdbj.org/pub/pdb/validation_reports/p5/7p50 | HTTPS FTP |
-Related structure data
Related structure data | 7p4vC 7p4yC 7p52C 2j9dS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | 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) |
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-Non-polymers , 7 types, 526 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MES / | #6: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.24 % / Description: Transparent spike |
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Crystal grow | Temperature: 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
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99985 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99985 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.74 Å2 / Biso mean: 20.8654 Å2 / Biso min: 8.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.16→57.33 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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