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Yorodumi- PDB-2hfu: Crystal structure of L. major mevalonate kinase in complex with R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hfu | ||||||
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Title | Crystal structure of L. major mevalonate kinase in complex with R-mevalonate | ||||||
Components | Mevalonate kinase, putative | ||||||
Keywords | TRANSFERASE / GHMP kinase / mevalonate kinase / Trypanosomatid parasite | ||||||
Function / homology | Function and homology information mevalonate kinase / mevalonate kinase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol biosynthetic process / glycosome / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sgraja, T. / Hunter, W.N. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2007 Title: Structure, substrate recognition and reactivity of Leishmania major mevalonate kinase. Authors: Sgraja, T. / Smith, T.K. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hfu.cif.gz | 152.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hfu.ent.gz | 119.3 KB | Display | PDB format |
PDBx/mmJSON format | 2hfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/2hfu ftp://data.pdbj.org/pub/pdb/validation_reports/hf/2hfu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological unit is a monomer. There are 2 biological units in the asymmetric unit. |
-Components
#1: Protein | Mass: 35811.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q4Q6K7, mevalonate kinase #2: Chemical | ChemComp-MEV / ( | #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: 2.19 Å3/Da / Density % sol: 43.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 1.2M sodium citrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 29, 2005 / Details: mirrors |
Radiation | Monochromator: Si channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→39.253 Å / Num. all: 39420 / Num. obs: 39420 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.297 / % possible all: 89.4 |
-Phasing
Phasing MR | Rfactor: 0.331 / Cor.coef. Fo:Fc: 0.677
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Selenomethionine derivative of the L. major mevalonate kinase Resolution: 2→36.49 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.648 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.353 Å2
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Refinement step | Cycle: LAST / Resolution: 2→36.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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