+Open data
-Basic information
Entry | Database: PDB / ID: 7ns8 | ||||||||||||
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Title | Triphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius | ||||||||||||
Components | Triphosphate tunnel metalloenzyme Saci_0718 | ||||||||||||
Keywords | HYDROLASE / TTM / CYTH | ||||||||||||
Function / homology | Adenylyl cyclase CyaB / CYTH / CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily / ATP binding / metal ion binding / Conserved Archaeal protein Function and homology information | ||||||||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 7ns8.cif.gz | 95.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ns8.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ns8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ns8_validation.pdf.gz | 450.3 KB | Display | wwPDB validaton report |
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Full document | 7ns8_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 7ns8_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 7ns8_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/7ns8 ftp://data.pdbj.org/pub/pdb/validation_reports/ns/7ns8 | HTTPS FTP |
-Related structure data
Related structure data | 7ns9C 7nsaC 7nsdC 7nsfC 7oa2C 2eenS 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 on special symmetry positions |
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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-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q4JAT2 | ||||
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#2: Chemical | ChemComp-CXS / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: Reservoir: 0.2 M Lithium sulfate, 0.1 M CAPS pH 10.5, 2 M Ammonium sulfate Protein 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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979003 Å |
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: 0.979003 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→44.4 Å / Num. obs: 11068 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 34.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01105 / Rrim(I) all: 0.01563 / Net I/σ(I): 29.77 |
Reflection shell | Resolution: 2.3→2.383 Å / Num. unique obs: 1074 / CC1/2: 0.993 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EEN Resolution: 2.3→44.4 Å / SU ML: 0.2299 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.867 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: 41.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→44.4 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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