+Open data
-Basic information
Entry | Database: PDB / ID: 4krd | ||||||
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Title | Crystal Structure of Pho85-Pcl10 Complex | ||||||
Components |
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Keywords | Transferase/Signaling Protein / Glycogen Synthesis / CDK / cyclin / Glycogen Synthesis Regulation / Transferase-Signaling Protein complex | ||||||
Function / homology | Function and homology information establishment or maintenance of cytoskeleton polarity / Pho85-Pho80 CDK-cyclin complex / negative regulation of phosphate metabolic process / regulation of establishment or maintenance of cell polarity / regulation of cell cycle phase transition / long-chain fatty acid metabolic process / positive regulation of phospholipid biosynthetic process / fungal-type cell wall organization / regulation of glycogen biosynthetic process / regulation of nucleocytoplasmic transport ...establishment or maintenance of cytoskeleton polarity / Pho85-Pho80 CDK-cyclin complex / negative regulation of phosphate metabolic process / regulation of establishment or maintenance of cell polarity / regulation of cell cycle phase transition / long-chain fatty acid metabolic process / positive regulation of phospholipid biosynthetic process / fungal-type cell wall organization / regulation of glycogen biosynthetic process / regulation of nucleocytoplasmic transport / negative regulation of glycogen biosynthetic process / cell cycle G1/S phase transition / cellular bud neck / negative regulation of calcium-mediated signaling / cyclin-dependent protein serine/threonine kinase regulator activity / negative regulation of macroautophagy / glycogen metabolic process / regulation of cell division / lipid homeostasis / positive regulation of macroautophagy / regulation of lipid metabolic process / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / protein destabilization / regulation of protein stability / G1/S transition of mitotic cell cycle / regulation of protein localization / regulation of cell cycle / protein kinase activity / protein serine kinase activity / DNA damage response / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.952 Å | ||||||
Authors | Quiocho, F.A. / Zheng, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: New Structural Insights into Phosphorylation-free Mechanism for Full Cyclin-dependent Kinase (CDK)-Cyclin Activity and Substrate Recognition. Authors: Zheng, F. / Quiocho, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4krd.cif.gz | 208.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4krd.ent.gz | 166.2 KB | Display | PDB format |
PDBx/mmJSON format | 4krd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4krd_validation.pdf.gz | 435.6 KB | Display | wwPDB validaton report |
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Full document | 4krd_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 4krd_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 4krd_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/4krd ftp://data.pdbj.org/pub/pdb/validation_reports/kr/4krd | HTTPS FTP |
-Related structure data
Related structure data | 4krcC 2pk9S 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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Details | Heterodimer is composed of one molecular Pho85 and one molecular Pcl10 |
-Components
#1: Protein | Mass: 36356.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: P7102.18A, PHO85, SSG3, YPL031C / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P17157, cyclin-dependent kinase |
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#2: Protein | Mass: 23752.602 Da / Num. of mol.: 1 / Fragment: UNP residues 227-433 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: G2838, PCL10, YGL134W / Plasmid: pSBET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P53124 |
#3: 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: 2.17 Å3/Da / Density % sol: 43.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 22-25% Polyethylene glycol 5000 monomethyl ether (PEG 5K MME), 0.1 M 2-morpholinoethanesulfonic acid (MES), pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2006 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.952→49.925 Å / Num. all: 37631 / Num. obs: 35878 / % possible obs: 95.34 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.332 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PK9 Resolution: 1.952→49.925 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 24.25 / 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 / Bsol: 60.264 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.952→49.925 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 7.6862 Å / Origin y: -13.3166 Å / Origin z: 22.4181 Å
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Refinement TLS group | Selection details: all |