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Yorodumi- PDB-4f4j: Conversion of the enzyme guanylate kinase into a mitotic spindle ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f4j | |||||||||
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Title | Conversion of the enzyme guanylate kinase into a mitotic spindle orienting protein by a single mutation that inhibits gmp- induced closing | |||||||||
Components | Guanylate kinase | |||||||||
Keywords | TRANSFERASE / Phosphotransferase / GMP and ATP | |||||||||
Function / homology | Function and homology information Azathioprine ADME / GDP biosynthetic process / Interconversion of nucleotide di- and triphosphates / guanylate kinase / purine nucleotide metabolic process / guanylate kinase activity / phosphorylation / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | |||||||||
Authors | Johnston, C.A. / Whitney, D. / Volkman, B.F. / Prehoda, K.E. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Conversion of the enzyme guanylate kinase into a mitotic-spindle orienting protein by a single mutation that inhibits GMP-induced closing. Authors: Johnston, C.A. / Whitney, D.S. / Volkman, B.F. / Doe, C.Q. / Prehoda, K.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f4j.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f4j.ent.gz | 126.2 KB | Display | PDB format |
PDBx/mmJSON format | 4f4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/4f4j ftp://data.pdbj.org/pub/pdb/validation_reports/f4/4f4j | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22419.205 Da / Num. of mol.: 2 / Fragment: GMP kinase (unp residues 1-187) / Mutation: S35P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: GUK1, YDR454C, D9461.39 / Production host: Escherichia coli (E. coli) / References: UniProt: P15454, guanylate kinase #2: Chemical | ChemComp-SO4 / #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: 3.92 Å3/Da / Density % sol: 68.64 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.6M LiSO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: Jun 16, 2011 |
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: 2.45→50 Å / Num. all: 25356 / Num. obs: 24012 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.914 / SU B: 14.769 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.258 / ESU R Free: 0.221 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.682 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.514 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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