+Open data
-Basic information
Entry | Database: PDB / ID: 1ve5 | ||||||
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Title | Crystal Structure of T.th. HB8 Threonine deaminase | ||||||
Components | Threonine deaminaseThreonine ammonia-lyase | ||||||
Keywords | LYASE / threonine deaminase catabolic / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information amino acid metabolic process / pyridoxal phosphate binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Goto, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of T.th. HB8 Threonine deaminase 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 | 1ve5.cif.gz | 224.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ve5.ent.gz | 181.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ve5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/1ve5 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/1ve5 | 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: 32818.926 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RP / References: UniProt: Q5SLL4, threonine ammonia-lyase #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-PLP / #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: 2.46 Å3/Da / Density % sol: 49.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, MPD, Ca(Ace)2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 31, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. all: 67964 / Num. obs: 65660 / % possible obs: 95.7 % / Biso Wilson estimate: 21.4 Å2 |
Reflection shell | Resolution: 2.15→2.27 Å / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→10 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1479234.77 / 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: 78.4462 Å2 / ksol: 0.424325 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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