+Open data
-Basic information
Entry | Database: PDB / ID: 8tfo | ||||||
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Title | Structure of MKvar | ||||||
Components | Mevalonate kinase | ||||||
Keywords | TRANSFERASE / extremo-tolerant / psychrophilic | ||||||
Function / homology | Function and homology information mevalonate kinase / mevalonate kinase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol biosynthetic process / phosphorylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Ramazzottius varieornatus (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Peat, T.S. / Newman, J. / Esquirol, L. / Nebl, T. / Scott, C. / Vickers, C. / Sainsbury, F. | ||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2024 Title: Characterization of novel mevalonate kinases from the tardigrade Ramazzottius varieornatus and the psychrophilic archaeon Methanococcoides burtonii. Authors: Esquirol, L. / Newman, J. / Nebl, T. / Scott, C. / Vickers, C. / Sainsbury, F. / Peat, T.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tfo.cif.gz | 169.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tfo.ent.gz | 127.8 KB | Display | PDB format |
PDBx/mmJSON format | 8tfo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tfo_validation.pdf.gz | 1018.5 KB | Display | wwPDB validaton report |
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Full document | 8tfo_full_validation.pdf.gz | 1022.3 KB | Display | |
Data in XML | 8tfo_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 8tfo_validation.cif.gz | 40.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/8tfo ftp://data.pdbj.org/pub/pdb/validation_reports/tf/8tfo | HTTPS FTP |
-Related structure data
Related structure data | 8tebC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 405 / Label seq-ID: 10 - 414
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 45339.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ramazzottius varieornatus (invertebrata) Gene: RvY_15762-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D1VW28 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.08 Å3/Da / Density % sol: 40.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: Protein bound to mevalonate at about 3 mg/mL was set up in 150 nL plus 150 nL drops over 50 microlitres of reservoir which contained: 0.126 M calcium acetate, 24.9 v/v PEG 400, 0.09 M sodium ...Details: Protein bound to mevalonate at about 3 mg/mL was set up in 150 nL plus 150 nL drops over 50 microlitres of reservoir which contained: 0.126 M calcium acetate, 24.9 v/v PEG 400, 0.09 M sodium HEPES pH 8.4 with 10 mM taurine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953723 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953723 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.1 Å / Num. obs: 52511 / % possible obs: 99.8 % / Redundancy: 27.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.057 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 26.8 % / Rmerge(I) obs: 4.656 / Mean I/σ(I) obs: 1 / Num. unique obs: 3787 / CC1/2: 0.623 / Rpim(I) all: 0.9 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.091 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.174 / SU B: 7.226 / SU ML: 0.181 / Average fsc free: 0.9403 / Average fsc work: 0.9525 / Cross valid method: FREE R-VALUE / ESU R: 0.208 / ESU R Free: 0.176 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.413 Å2
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Refinement step | Cycle: LAST / Resolution: 2→44.091 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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