+Open data
-Basic information
Entry | Database: PDB / ID: 4xhg | ||||||
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Title | Structure of C. glabrata Hrr25 bound to ADP (formate condition) | ||||||
Components | Similar to uniprot|P29295 Saccharomyces cerevisiae YPL204w HRR25 | ||||||
Keywords | TRANSFERASE / casein kinase / monopolin | ||||||
Function / homology | Function and homology information regulation of vesicle fusion with Golgi apparatus / regulation of protein localization by the Cvt pathway / monopolin complex / positive regulation of clathrin-dependent endocytosis / spindle attachment to meiosis I kinetochore / regulation of ER to Golgi vesicle-mediated transport / tRNA wobble uridine modification / cellular bud tip / pexophagy / cellular bud neck ...regulation of vesicle fusion with Golgi apparatus / regulation of protein localization by the Cvt pathway / monopolin complex / positive regulation of clathrin-dependent endocytosis / spindle attachment to meiosis I kinetochore / regulation of ER to Golgi vesicle-mediated transport / tRNA wobble uridine modification / cellular bud tip / pexophagy / cellular bud neck / regulation of autophagosome assembly / spindle pole body / preribosome, small subunit precursor / ribosomal large subunit biogenesis / ribosomal small subunit biogenesis / peroxisome / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / DNA repair / protein serine/threonine kinase activity / Golgi apparatus / ATP binding / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Candida glabrata (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Ye, Q. / Corbett, K.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Embo J. / Year: 2016 Title: Structure of the Saccharomyces cerevisiae Hrr25:Mam1 monopolin subcomplex reveals a novel kinase regulator. Authors: Ye, Q. / Ur, S.N. / Su, T.Y. / Corbett, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xhg.cif.gz | 165.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xhg.ent.gz | 127.9 KB | Display | PDB format |
PDBx/mmJSON format | 4xhg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xhg_validation.pdf.gz | 774.2 KB | Display | wwPDB validaton report |
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Full document | 4xhg_full_validation.pdf.gz | 779.3 KB | Display | |
Data in XML | 4xhg_validation.xml.gz | 18 KB | Display | |
Data in CIF | 4xhg_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/4xhg ftp://data.pdbj.org/pub/pdb/validation_reports/xh/4xhg | HTTPS FTP |
-Related structure data
Related structure data | 4xh0SC 4xhhC 4xhlC 5cyzC 5czoC S: Starting model for refinement 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: 46750.430 Da / Num. of mol.: 1 / Fragment: UNP residues 1-403 / Mutation: K38R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida glabrata (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FS46 |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-FMT / |
#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: 2.49 Å3/Da / Density % sol: 50.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 6.5, 0.2 M sodium formate, 15% PEG 3350, and 5 mM TCEP. Cryoprotected with 20% glycerol. PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2013 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→44.6 Å / Num. obs: 25960 / % possible obs: 99.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.5 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XH0 Resolution: 2.15→44.6 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.97 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→44.6 Å
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Refine LS restraints |
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LS refinement shell |
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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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