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Yorodumi- PDB-8ork: cyclic 2,3-diphosphoglycerate synthetase from the hyperthermophil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ork | ||||||
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Title | cyclic 2,3-diphosphoglycerate synthetase from the hyperthermophilic archaeon Methanothermus fervidus | ||||||
Components | Cyclic 2,3-diphosphoglycerate synthetase | ||||||
Keywords | LIGASE / Synthetase / extremolyte / thermophilic | ||||||
Function / homology | cyclic 2,3-diphosphoglycerate synthase / cyclic 2,3-diphosphoglycerate synthetase activity / Cyclic 2, 3-diphospoglycerate synthetase / ligase activity / gluconeogenesis / ATP binding / cytoplasm / DI(HYDROXYETHYL)ETHER / Cyclic 2,3-diphosphoglycerate synthetase Function and homology information | ||||||
Biological species | Methanothermus fervidus DSM 2088 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.64 Å | ||||||
Authors | De Rose, S.A. / Isupov, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Front Microbiol / Year: 2023 Title: Structural characterization of a novel cyclic 2,3-diphosphoglycerate synthetase involved in extremolyte production in the archaeon Methanothermus fervidus . Authors: De Rose, S.A. / Isupov, M.N. / Worthy, H.L. / Stracke, C. / Harmer, N.J. / Siebers, B. / Littlechild, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ork.cif.gz | 219.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ork.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ork.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ork_validation.pdf.gz | 474.9 KB | Display | wwPDB validaton report |
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Full document | 8ork_full_validation.pdf.gz | 482.5 KB | Display | |
Data in XML | 8ork_validation.xml.gz | 23 KB | Display | |
Data in CIF | 8ork_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/8ork ftp://data.pdbj.org/pub/pdb/validation_reports/or/8ork | HTTPS FTP |
-Related structure data
Related structure data | 8oruC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 51418.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermus fervidus DSM 2088 (archaea) Gene: cpgS, Mfer_0077 / Plasmid: pLATE51 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O93732, cyclic 2,3-diphosphoglycerate synthase |
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-Non-polymers , 6 types, 323 molecules
#2: Chemical | ChemComp-MPO / | ||||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 2.99 Å3/Da / Density % sol: 58.81 % |
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Crystal grow | Temperature: 292.15 K / Method: microbatch / pH: 7.5 Details: Morpheus condition F7 consisting of 0.12 M Monosaccharides mix; 0.1M Buffer System 2 pH 7.5; 30% v/v Precipitant Mix 3 Buffer system 2: Sodium HEPES; MOPS (acid) pH7.5 Monosaccharides mix: 0. ...Details: Morpheus condition F7 consisting of 0.12 M Monosaccharides mix; 0.1M Buffer System 2 pH 7.5; 30% v/v Precipitant Mix 3 Buffer system 2: Sodium HEPES; MOPS (acid) pH7.5 Monosaccharides mix: 0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D-Xylose; 0.2M N-Acetyl-D-Glucosamine Precipitants mix 3: 40% v/v Glycerol; 20% w/v PEG 4000 Temp details: Memmert crystals incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→42.71 Å / Num. obs: 75512 / % possible obs: 95.98 % / Redundancy: 5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.038 / Rrim(I) all: 0.086 / Net I/av σ(I): 8 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.64→1.68 Å / Redundancy: 5 % / Num. unique obs: 3134 / CC1/2: 0.28 / % possible all: 60.03 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.64→42.71 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.64→42.71 Å
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