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Yorodumi- PDB-5gme: Crystal structure of Sulfolobus solfataricus Diphosphomevalonate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gme | ||||||
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Title | Crystal structure of Sulfolobus solfataricus Diphosphomevalonate decarboxylase in complex with ADP | ||||||
Components | Diphosphomevalonate decarboxylase | ||||||
Keywords | LYASE / Sulfolobus solfataricus / Diphosphomevalonate decarboxylase / ADP | ||||||
Function / homology | Function and homology information diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Unno, H. / Hemmi, H. / Hattori, A. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: A Single Amino Acid Mutation Converts (R)-5-Diphosphomevalonate Decarboxylase into a Kinase Authors: Motoyama, K. / Unno, H. / Hattori, A. / Takaoka, T. / Ishikita, H. / Kawaide, H. / Yoshimura, T. / Hemmi, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gme.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gme.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 5gme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gme_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5gme_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5gme_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 5gme_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/5gme ftp://data.pdbj.org/pub/pdb/validation_reports/gm/5gme | HTTPS FTP |
-Related structure data
Related structure data | 5gmdC 4z7cS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37079.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO2989 / Production host: Escherichia coli (E. coli) References: UniProt: Q97UL5, diphosphomevalonate decarboxylase |
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-Non-polymers , 5 types, 262 molecules
#2: Chemical | ChemComp-DP6 / ( | ||
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#3: Chemical | ChemComp-ADP / | ||
#4: Chemical | ChemComp-AMP / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.6 / Details: 0.1M sodium acetate, 1.5M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→27.8 Å / Num. obs: 50337 / % possible obs: 99.8 % / Redundancy: 15.2 % / Net I/σ(I): 23 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4Z7C Resolution: 1.7→27.75 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.607 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.579 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→27.75 Å
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Refine LS restraints |
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