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- PDB-8oru: cyclic 2,3-diphosphoglycerate synthetase from the hyperthermophil... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8oru | ||||||
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Title | cyclic 2,3-diphosphoglycerate synthetase from the hyperthermophilic archaeon Methanothermus fervidus bound to 2,3-diphosphoglycerate and ADP. | ||||||
![]() | Cyclic 2,3-diphosphoglycerate synthetase | ||||||
![]() | LIGASE / Synthetase / extremolyte / thermophilic | ||||||
Function / homology | ![]() cyclic 2,3-diphosphoglycerate synthase / cyclic 2,3-diphosphoglycerate synthetase activity / ligase activity / gluconeogenesis / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | De Rose, S.A. / Isupov, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 717.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 6.8 MB | Display | ![]() |
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Full document | ![]() | 6.7 MB | Display | |
Data in XML | ![]() | 61 KB | Display | |
Data in CIF | ![]() | 82.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8orkC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules AAABBBCCCDDD
#1: Protein | Mass: 50724.703 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cpgS, Mfer_0077 / Production host: ![]() ![]() References: UniProt: O93732, cyclic 2,3-diphosphoglycerate synthase |
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-Non-polymers , 6 types, 80 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DG2.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DG2.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-DG2 / ( #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-PO4 / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.03 % |
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Crystal grow | Temperature: 292.15 K / Method: microbatch / pH: 8.5 Details: The substrate bound crystals grew in condition E12 of the Morpheus screen consisting of 0.12M Ethylene glycols mix, 0.1M Buffer System 3 pH 8.5 and 37.5% v/v of Precipitant Mix 4. where the ...Details: The substrate bound crystals grew in condition E12 of the Morpheus screen consisting of 0.12M Ethylene glycols mix, 0.1M Buffer System 3 pH 8.5 and 37.5% v/v of Precipitant Mix 4. where the different solution are: Ethylene glycols mix: 0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol. Buffer system 3: Tris (base); BICINE pH 8.5 Precipitant mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→69.92 Å / Num. obs: 92153 / % possible obs: 97.7 % / Redundancy: 1.8 % / CC1/2: 0.986 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.115 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.23→2.27 Å / Redundancy: 1.9 % / Num. unique obs: 4558 / CC1/2: 0.382 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.23→69.92 Å
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