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Yorodumi- PDB-1yak: Complex of Bacillus subtilis TenA with 4-amino-2-methyl-5-hydroxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yak | ||||||
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Title | Complex of Bacillus subtilis TenA with 4-amino-2-methyl-5-hydroxymethylpyrimidine | ||||||
Components | Transcriptional activator tenA | ||||||
Keywords | TRANSCRIPTION / thiaminase | ||||||
Function / homology | Function and homology information aminopyrimidine aminohydrolase / thiaminase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Toms, A.V. / Haas, A.L. / Park, J.-H. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structural characterization of the regulatory proteins TenA and TenI from Bacillus subtilis and identification of TenA as a thiaminase II. Authors: Toms, A.V. / Haas, A.L. / Park, J.H. / Begley, T.P. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yak.cif.gz | 178.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yak.ent.gz | 144.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/1yak ftp://data.pdbj.org/pub/pdb/validation_reports/ya/1yak | HTTPS FTP |
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-Related structure data
Related structure data | 1yadC 1yafSC 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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2 |
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Unit cell |
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Details | The biological assembly is a tetramer. The asymmetric unit contains 2 half biological units. |
-Components
#1: Protein | Mass: 30569.998 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: tenA / Plasmid: pDESTF1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25052 #2: Chemical | ChemComp-HMH / #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: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 0.7 M 1,6-hexanediol, 10 mM MgCl2, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 8, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 33460 / Num. obs: 33417 / % possible obs: 93.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 28.8 Å2 / Rsym value: 0.063 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.5→2.66 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4072 / Rsym value: 0.264 / % possible all: 68.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YAF Resolution: 2.5→49.39 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3184563.21 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.49 Å2 / ksol: 0.358823 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→49.39 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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