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- PDB-7ns9: Triphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ns9 | ||||||||||||
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Title | Triphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius in complex with triphosphate and calcium | ||||||||||||
![]() | Triphosphate tunnel metalloenzyme Saci_0718 | ||||||||||||
![]() | HYDROLASE / TTM / CYTH / triphosphate / calcium | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Vogt, M.S. / Essen, L.-O. / Banerjee, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The archaeal triphosphate tunnel metalloenzyme SaTTM defines structural determinants for the diverse activities in the CYTH protein family. Authors: Vogt, M.S. / Ngouoko Nguepbeu, R.R. / Mohr, M.K.F. / Albers, S.V. / Essen, L.O. / Banerjee, A. #1: ![]() Title: The archaeal triphosphate tunnel metalloenzyme Sa TTM defines structural determinants for the diverse activities in the CYTH protein family Authors: Vogt, M.S. / Nguepbeu, R.R.N. / Mohr, M.K.F. / Albers, S.V. / Essen, L.O. / Banerjee, 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 | ![]() | 139.9 KB | Display | ![]() |
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PDB format | ![]() | 100.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ns8C ![]() 7nsaC ![]() 7nsdC ![]() 7nsfC ![]() 7oa2C ![]() 2eenS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23698.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 Gene: Saci_0718 Production host: ![]() ![]() References: UniProt: Q4JAT2 |
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-Non-polymers , 5 types, 142 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/3PO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/3PO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACT / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-3PO / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 59.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: Reservoir: 0.2 M NaCl, 0.1 M Na/KPO4 pH 6.2, 20% (w/v) PEG 1000 buffer: 200 mM NaCl, 50 mM Tris, pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→46 Å / Num. obs: 25885 / % possible obs: 94.31 % / Redundancy: 2 % / Biso Wilson estimate: 32.86 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.44 |
Reflection shell | Resolution: 1.75→1.813 Å / Num. unique obs: 2581 / CC1/2: 0.352 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2EEN Resolution: 1.75→46 Å / SU ML: 0.2044 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9101 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 51.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→46 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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