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Yorodumi- PDB-2phk: THE CRYSTAL STRUCTURE OF A PHOSPHORYLASE KINASE PEPTIDE SUBSTRATE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2phk | ||||||
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Title | THE CRYSTAL STRUCTURE OF A PHOSPHORYLASE KINASE PEPTIDE SUBSTRATE COMPLEX: KINASE SUBSTRATE RECOGNITION | ||||||
Components |
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Keywords | COMPLEX (TRANSFERASE/PEPTIDE) / CATALYTIC MECHANISM / DIMERIZATION / PHOSPHORYLASE KINASE / REVERSIBLE PHOSPHORYLISATION / SUBSTRATE RECOGNITION / COMPLEX (TRANSFERASE-PEPTIDE) / COMPLEX (TRANSFERASE-PEPTIDE) complex | ||||||
Function / homology | Function and homology information phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / tau-protein kinase / glycogen biosynthetic process / tau-protein kinase activity / skeletal muscle myofibril / calmodulin binding / non-specific serine/threonine protein kinase / phosphorylation ...phosphorylase kinase / phosphorylase kinase activity / phosphorylase kinase complex / tau-protein kinase / glycogen biosynthetic process / tau-protein kinase activity / skeletal muscle myofibril / calmodulin binding / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / ATP binding Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Lowe, E.D. / Noble, M.E.M. / Skamnaki, V.T. / Oikonomakos, N.G. / Owen, D.J. / Johnson, L.N. | ||||||
Citation | Journal: EMBO J. / Year: 1997 Title: The crystal structure of a phosphorylase kinase peptide substrate complex: kinase substrate recognition. Authors: Lowe, E.D. / Noble, M.E. / Skamnaki, V.T. / Oikonomakos, N.G. / Owen, D.J. / Johnson, L.N. #1: Journal: Structure / Year: 1995 Title: Two Structures of the Catalytic Domain of Phosphorylase Kinase: An Active Protein Kinase Complexed with Substrate Analogue and Product Authors: Owen, D.J. / Noble, M.E. / Garman, E.F. / Papageorgiou, A.C. / Johnson, L.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2phk.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2phk.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 2phk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/2phk ftp://data.pdbj.org/pub/pdb/validation_reports/ph/2phk | HTTPS FTP |
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-Related structure data
Related structure data | 1phkS 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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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 31983.758 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Strain: NEW ZEALAND WHITE / Tissue: SKELETAL MUSCLE / Cell line: BL21 / Gene: PHKG / Organ: SKELETALSkeleton / Plasmid: PMW172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P00518, EC: 2.7.1.38 |
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#2: Protein/peptide | Mass: 939.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 90 molecules
#3: Chemical | #4: Chemical | ChemComp-ATP / | #5: Chemical | ChemComp-GOL / | #6: 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: 2.7 Å3/Da / Density % sol: 54.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.9 / Details: pH 6.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9 |
Detector | Type: XRII / Detector: CCD AREA DETECTOR / Date: Mar 11, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 10062 / % possible obs: 86.3 % / Observed criterion σ(I): 2 / Redundancy: 2.15 % / Rmerge(I) obs: 0.098 / Rsym value: 0.089 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.397 / % possible all: 78.1 |
Reflection | *PLUS Num. measured all: 21644 |
Reflection shell | *PLUS % possible obs: 78.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PHK Resolution: 2.6→25 Å / σ(F): 0.3
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Refinement step | Cycle: LAST / Resolution: 2.6→25 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||
Refinement | *PLUS | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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