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Yorodumi- PDB-4rkp: Crystal Structure of Mevalonate-3-Kinase from Thermoplasma acidop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rkp | ||||||
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Title | Crystal Structure of Mevalonate-3-Kinase from Thermoplasma acidophilum (apo form) | ||||||
Components | Putative uncharacterized protein Ta1305 | ||||||
Keywords | TRANSFERASE / mevalonate / mevalonate-3-kinase / mevalonate pyrophosphate decarboxylase / mevalonate diphosphate decarboxylase / mevalonic acid / mevalonate kinase | ||||||
Function / homology | Function and homology information mevalonate 3-kinase / isopentenyl diphosphate biosynthetic process, mevalonate pathway / phosphotransferase activity, alcohol group as acceptor / kinase activity / ATP binding Similarity search - Function | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Vinokur, J.M. / Cascio, D. / Sawaya, M.R. / Bowie, J.U. | ||||||
Citation | Journal: Protein Sci. / Year: 2015 Title: Structural analysis of mevalonate-3-kinase provides insight into the mechanisms of isoprenoid pathway decarboxylases. Authors: Vinokur, J.M. / Korman, T.P. / Sawaya, M.R. / Collazo, M. / Cascio, D. / Bowie, J.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rkp.cif.gz | 138.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rkp.ent.gz | 106.1 KB | Display | PDB format |
PDBx/mmJSON format | 4rkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rkp_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 4rkp_full_validation.pdf.gz | 453.4 KB | Display | |
Data in XML | 4rkp_validation.xml.gz | 24 KB | Display | |
Data in CIF | 4rkp_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/4rkp ftp://data.pdbj.org/pub/pdb/validation_reports/rk/4rkp | HTTPS FTP |
-Related structure data
Related structure data | 4rksC 4rkzC 1fi4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37278.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165 Gene: Ta1305 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HIN1 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.71 Å3/Da / Density % sol: 54.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: ProComplex condition 68, (Qiagen Cat No. 135468A) 0.1 M Sodium Acetate, pH 5.0, 1.0 M Ammonium Sulfate (2:1 Protein:Reservoir ratio), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 25, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: CONFOCAL MIRRORS Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→62.59 Å / Num. all: 54102 / Num. obs: 54102 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.37 % / Biso Wilson estimate: 27.22 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 14.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FI4 Resolution: 2.1→62.588 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 22.66 / Stereochemistry target values: ML
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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: 33.7771 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→62.588 Å
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Refine LS restraints |
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LS refinement shell |
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