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Yorodumi- PDB-2x7i: Crystal structure of mevalonate kinase from methicillin-resistant... -
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-Basic information
Entry | Database: PDB / ID: 2x7i | ||||||
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Title | Crystal structure of mevalonate kinase from methicillin-resistant Staphylococcus aureus MRSA252 | ||||||
Components | MEVALONATE KINASE | ||||||
Keywords | TRANSFERASE / KINASE | ||||||
Function / homology | GHMP kinase, C-terminal domain / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / CITRIC ACID / Mevalonate kinase / Mevalonate kinase Function and homology information | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å | ||||||
Authors | Oke, M. / Yan, X. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H. | ||||||
Citation | Journal: J.Struct.Funct.Genomics / Year: 2010 Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs. Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x7i.cif.gz | 127.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x7i.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 2x7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x7i_validation.pdf.gz | 451.9 KB | Display | wwPDB validaton report |
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Full document | 2x7i_full_validation.pdf.gz | 455 KB | Display | |
Data in XML | 2x7i_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 2x7i_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/2x7i ftp://data.pdbj.org/pub/pdb/validation_reports/x7/2x7i | HTTPS FTP |
-Related structure data
Related structure data | 2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2xu2C 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33115.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: MRSA252 / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6GJ78, UniProt: A0A7U7EU40*PLUS |
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#2: Chemical | ChemComp-CIT / |
#3: Chemical | ChemComp-CL / |
#4: 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: 3.3 Å3/Da / Density % sol: 62.3 % / Description: NONE |
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Crystal grow | pH: 4 Details: 0.1 M CITRIC ACID PH 4.0, 3.6 M SODIUM CHLORIDE. THE CRYSTALS WERE CRYOPROTECTED BY ADDING 25% PEG400 INTO THE SCREEN SOLUTION. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.6 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 27, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→81.92 Å / Num. obs: 17784 / % possible obs: 80.3 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 50.2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: NONE Resolution: 2.2→81.92 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 14.053 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ORDERED FROM RESIDUE 2-306. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.542 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→81.92 Å
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Refine LS restraints |
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