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Yorodumi- PDB-6n0y: Crystal structure of Anaerolinea thermophila mevalonate 5-phospha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n0y | |||||||||
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Title | Crystal structure of Anaerolinea thermophila mevalonate 5-phosphate decarboxylase complexed with (R)-MVAPP | |||||||||
Components | Diphosphomevalonate decarboxylase | |||||||||
Keywords | LYASE | |||||||||
Function / homology | Function and homology information diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / phosphorylation / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | Anaerolinea thermophila | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Noel, J.P. / Thomas, S.T. / Louie, G.V. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2019 Title: Substrate Specificity and Engineering of Mevalonate 5-Phosphate Decarboxylase. Authors: Thomas, S.T. / Louie, G.V. / Lubin, J.W. / Lundblad, V. / Noel, J.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n0y.cif.gz | 399.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n0y.ent.gz | 328.2 KB | Display | PDB format |
PDBx/mmJSON format | 6n0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/6n0y ftp://data.pdbj.org/pub/pdb/validation_reports/n0/6n0y | HTTPS FTP |
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-Related structure data
Related structure data | 6n0xC 6n0zC 6n10C 2hk2S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 35744.645 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anaerolinea thermophila (strain DSM 14523 / JCM 11388 / NBRC 100420 / UNI-1) (bacteria) Strain: DSM 14523 / JCM 11388 / NBRC 100420 / UNI-1 / Gene: mvaD, ANT_19910 / Production host: Escherichia coli (E. coli) References: UniProt: E8N6F3, diphosphomevalonate decarboxylase #2: Chemical | ChemComp-DP6 / ( #3: Water | ChemComp-HOH / | |
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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: 2.72 Å3/Da / Density % sol: 54.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M acetic acid pH 4.5 3-5% PEG 20,000 0.3 M ammonium acetate 5 mM (R)-MVAPP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2014 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→52.075 Å / Num. obs: 103991 / % possible obs: 89.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.457 / Num. unique obs: 3426 / % possible all: 59.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HK2 Resolution: 2.2→52.075 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 22.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→52.075 Å
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Refine LS restraints |
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LS refinement shell |
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