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Yorodumi- PDB-7oa2: Triphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oa2 | ||||||||||||
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Title | Triphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius in complex with pyrophosphate | ||||||||||||
Components | Triphosphate tunnel metalloenzyme Saci_0718 | ||||||||||||
Keywords | HYDROLASE / TTM / CYTH / triphosphate | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||||||||
Authors | Vogt, M.S. / Essen, L.-O. / Banerjee, A. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2021 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: Journal: Biorxiv / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oa2.cif.gz | 99.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oa2.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 7oa2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oa2_validation.pdf.gz | 723.5 KB | Display | wwPDB validaton report |
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Full document | 7oa2_full_validation.pdf.gz | 723.9 KB | Display | |
Data in XML | 7oa2_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 7oa2_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/7oa2 ftp://data.pdbj.org/pub/pdb/validation_reports/oa/7oa2 | HTTPS FTP |
-Related structure data
Related structure data | 7ns8C 7ns9SC 7nsaC 7nsdC 7nsfC 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
#1: Protein | Mass: 23698.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic) Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770 Gene: Saci_0718 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Gold / References: UniProt: Q4JAT2 |
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#2: Chemical | ChemComp-POP / |
#3: Chemical | ChemComp-K / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: Crystals were grown in 1:1 mixtures of JCSG Core IA11 (0.2M Potassium acetate, 20%(w/v) PEG 3350) and 10 mg/ml protein in 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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→45.91 Å / Num. obs: 6390 / % possible obs: 78.54 % / Redundancy: 1.9 % / Biso Wilson estimate: 58.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03404 / Rrim(I) all: 0.04814 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Num. unique obs: 636 / CC1/2: 0.778 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7NS9 Resolution: 2.7→45.91 Å / SU ML: 0.4615 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.1386 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: 61.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→45.91 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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