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Yorodumi- PDB-2ej0: Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ej0 | ||||||
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Title | Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase with Pyridoxamine 5'-phosphate | ||||||
Components | Branched-chain amino acid aminotransferase | ||||||
Keywords | TRANSFERASE / PLP-dependent enzyme | ||||||
Function / homology | Function and homology information aspartate biosynthetic process / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Goto, M. | ||||||
Citation | Journal: To be published Title: Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase with Pyridoxamine 5'-phosphate Authors: Goto, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ej0.cif.gz | 386 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ej0.ent.gz | 312.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ej0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ej0_validation.pdf.gz | 507.3 KB | Display | wwPDB validaton report |
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Full document | 2ej0_full_validation.pdf.gz | 529.9 KB | Display | |
Data in XML | 2ej0_validation.xml.gz | 81.1 KB | Display | |
Data in CIF | 2ej0_validation.cif.gz | 117 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/2ej0 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/2ej0 | HTTPS FTP |
-Related structure data
Related structure data | 1wrvS 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: 34072.957 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q5SM19, branched-chain-amino-acid transaminase #2: Chemical | ChemComp-PMP / #3: Chemical | ChemComp-MPD / ( #4: 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: 2.99 Å3/Da / Density % sol: 58.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: NaCl, MPD, Na Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→19.92 Å / Num. obs: 320144 / % possible obs: 99.3 % / Biso Wilson estimate: 17.5 Å2 |
Reflection shell | Resolution: 1.6→1.69 Å / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WRV Resolution: 1.6→19.84 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 3387372.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.0941 Å2 / ksol: 0.403845 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.003 / Total num. of bins used: 6
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Xplor file |
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