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Yorodumi- PDB-2p9t: Crystal Structure of Phosphoglycerate Kinase-2 bound to 3-phospho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p9t | ||||||
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Title | Crystal Structure of Phosphoglycerate Kinase-2 bound to 3-phosphoglycerate | ||||||
Components | Phosphoglycerate kinase, testis specific | ||||||
Keywords | TRANSFERASE / phosphoglycerate kinse / enzyme-substrate complex | ||||||
Function / homology | Function and homology information sperm fibrous sheath / Glycolysis / Gluconeogenesis / phosphoglycerate kinase / phosphoglycerate kinase activity / flagellated sperm motility / gluconeogenesis / glycolytic process / ADP binding / cilium ...sperm fibrous sheath / Glycolysis / Gluconeogenesis / phosphoglycerate kinase / phosphoglycerate kinase activity / flagellated sperm motility / gluconeogenesis / glycolytic process / ADP binding / cilium / phosphorylation / extracellular exosome / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sawyer, G.M. / Monzingo, A.F. / Poteet, E.C. / Robertus, J.D. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: X-ray analysis of phosphoglycerate kinase 2, a sperm-specific isoform from Mus musculus. Authors: Sawyer, G.M. / Monzingo, A.F. / Poteet, E.C. / O'Brien, D.A. / Robertus, J.D. | ||||||
History |
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Remark 999 | sequence There is a Gln -> Arg sequence conflict at residue 151 in the Uniprot database. Authors ...sequence There is a Gln -> Arg sequence conflict at residue 151 in the Uniprot database. Authors state that Protein sequence used in this PDB entry is from C3H/He strain which has Arg at residue 150, whereas UniProt sequence is from BALB/c strain that has Gln at residue 151. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p9t.cif.gz | 96.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p9t.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 2p9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p9t_validation.pdf.gz | 443.8 KB | Display | wwPDB validaton report |
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Full document | 2p9t_full_validation.pdf.gz | 449 KB | Display | |
Data in XML | 2p9t_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 2p9t_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/2p9t ftp://data.pdbj.org/pub/pdb/validation_reports/p9/2p9t | HTTPS FTP |
-Related structure data
Related structure data | 2p9qC 2paaC 1vjdS 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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-Components
#1: Protein | Mass: 44837.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: C3H/He / Gene: Pgk2, Pgk-2 / Plasmid: PGK-2-pGEX4T3 / Production host: Escherichia coli (E. coli) / References: UniProt: P09041, phosphoglycerate kinase |
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#2: Chemical | ChemComp-3PG / |
#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: 2.16 Å3/Da / Density % sol: 43.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10 mM D-3-phosphoglycerate, 30% PEG6000, 0.1 M Tris-Hcl, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 2006 / Details: BLUE MAX-FLUX CONFOCAL OPTICAL SYSTEM |
Radiation | Monochromator: BLUE MAX-FLUX CONFOCAL OPTICAL SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 24578 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 6 % / Rmerge(I) obs: 0.209 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VJD Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Bsol: 43.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å / Total num. of bins used: 24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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