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Yorodumi- PDB-2pb9: Crystal structure of C-terminal domain of phosphomethylpyrimidine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pb9 | ||||||
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Title | Crystal structure of C-terminal domain of phosphomethylpyrimidine kinase | ||||||
Components | Phosphomethylpyrimidine kinase | ||||||
Keywords | TRANSFERASE / phosphate / psi2 / 10417c / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information phosphomethylpyrimidine kinase activity / thiamine-phosphate diphosphorylase activity / thiamine biosynthetic process Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of C-terminal domain of phosphomethylpyrimidine kinase Authors: Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICAL UNIT ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pb9.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pb9.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 2pb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/2pb9 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/2pb9 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22869.697 Da / Num. of mol.: 2 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638, JCM 8422, Vc1 / Gene: PF1333 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U193 #2: Chemical | #3: 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: 2.59 Å3/Da / Density % sol: 52.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 2.0M Sodium formate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2007 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 13846 / Num. obs: 13846 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 24.8 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.484 / Num. unique all: 1328 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density and modeled as alanines.
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.042
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