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Yorodumi- PDB-2uzp: Crystal structure of the C2 domain of human protein kinase C gamma. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uzp | ||||||
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Title | Crystal structure of the C2 domain of human protein kinase C gamma. | ||||||
Components | PROTEIN KINASE C GAMMA TYPE | ||||||
Keywords | TRANSFERASE / METAL-BINDING / KINASE / ZINC-FINGER / ATP-BINDING / SPINOCEREBELLAR ATAXIA / CALCIUM-BINDING PROTEIN / SERINE/THREONINE-PROTEIN KINASE / PHOSPHOLIPID BINDING PROTEIN / NUCLEOTIDE-BINDING / PHORBOL- ESTER BINDING / PHOSPHORYLATION / PROTEIN KINASE C / NEURODEGENERATION | ||||||
Function / homology | Function and homology information Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / regulation of response to food / calcium,diacylglycerol-dependent serine/threonine kinase activity / positive regulation of mismatch repair / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / protein kinase C / chemosensory behavior / negative regulation of proteasomal protein catabolic process ...Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / regulation of response to food / calcium,diacylglycerol-dependent serine/threonine kinase activity / positive regulation of mismatch repair / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / protein kinase C / chemosensory behavior / negative regulation of proteasomal protein catabolic process / diacylglycerol-dependent serine/threonine kinase activity / innervation / regulation of phagocytosis / presynaptic cytosol / response to morphine / Calmodulin induced events / response to psychosocial stress / regulation of synaptic vesicle exocytosis / postsynaptic cytosol / response to pain / calyx of Held / negative regulation of protein ubiquitination / presynaptic modulation of chemical synaptic transmission / protein serine/threonine/tyrosine kinase activity / phosphorylation / synaptic membrane / negative regulation of protein catabolic process / regulation of circadian rhythm / long-term synaptic potentiation / response to toxic substance / G alpha (z) signalling events / rhythmic process / cell-cell junction / chemical synaptic transmission / negative regulation of neuron apoptotic process / learning or memory / postsynaptic density / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / perinuclear region of cytoplasm / zinc ion binding / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Pike, A.C.W. / Amos, A. / Johansson, C. / Sobott, F. / Savitsky, P. / Berridge, G. / Fedorov, O. / Umeano, C. / Gorrec, F. / Bunkoczi, G. ...Pike, A.C.W. / Amos, A. / Johansson, C. / Sobott, F. / Savitsky, P. / Berridge, G. / Fedorov, O. / Umeano, C. / Gorrec, F. / Bunkoczi, G. / Debreczeni, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Knapp, S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of C2 Domain of Protein Kinase C Gamma Authors: Pike, A.C.W. / Amos, A. / Johansson, C. / Sobott, F. / Savitsky, P. / Berridge, G. / Fedorov, O. / Umeano, C. / Gorrec, F. / Bunkoczi, G. / Debreczeni, J. / von Delft, F. / Arrowsmith, C.H. ...Authors: Pike, A.C.W. / Amos, A. / Johansson, C. / Sobott, F. / Savitsky, P. / Berridge, G. / Fedorov, O. / Umeano, C. / Gorrec, F. / Bunkoczi, G. / Debreczeni, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uzp.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uzp.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 2uzp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uzp_validation.pdf.gz | 464.4 KB | Display | wwPDB validaton report |
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Full document | 2uzp_full_validation.pdf.gz | 468.4 KB | Display | |
Data in XML | 2uzp_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 2uzp_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/2uzp ftp://data.pdbj.org/pub/pdb/validation_reports/uz/2uzp | HTTPS FTP |
-Related structure data
Related structure data | 1dsyS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 16533.654 Da / Num. of mol.: 3 / Fragment: C2 DOMAIN, RESIDUES 154-295 Source method: isolated from a genetically manipulated source Details: SCHIFFS BASE LINK BETWEEN SER -1 AND PYRIDOXAL PHOSPHATE PLP300 Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05129, protein kinase C |
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-Non-polymers , 6 types, 435 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | N-TERMINAL SER MET ARISE FROM VECTOR-ENCODED PROTEASE RECOGNITIO |
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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: 3.31 Å3/Da / Density % sol: 62.88 % |
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Crystal grow | pH: 6.5 Details: 1.8M AMMONIUM SULPHATE, 15MM COBALT CHLORIDE, 0.1M MES PH6.5, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 18, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2→56.08 Å / Num. obs: 45478 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 28.17 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DSY Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.117 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AMINO TERMINUS IS MODIFIED BY PYRIXODAL PHOSPHATE DURING CRYSTALLIZATION AND TIGHTLY COORDINATES A COBALT ION
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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: 31.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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