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Yorodumi- PDB-1j7g: Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j7g | ||||||
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Title | Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-tRNA(Tyr) deacylase | ||||||
Components | D-tyrosyl-tRNA(Tyr) deacylase | ||||||
Keywords | HYDROLASE / D-Tyr-tRNA(Tyr) deacylase / structural genomics / hypothetical protein / Structure 2 Function Project / S2F | ||||||
Function / homology | Function and homology information Ser(Gly)-tRNA(Ala) hydrolase activity / Gly-tRNA(Ala) hydrolase activity / D-tyrosyl-tRNA(Tyr) deacylase activity / D-aminoacyl-tRNA deacylase / tRNA metabolic process / D-amino acid catabolic process / aminoacyl-tRNA editing activity / tRNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Haemophilus influenzae Rd KW20 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAS / Resolution: 1.64 Å | ||||||
Authors | Lim, K. / Herzberg, O. / Structure 2 Function Project (S2F) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: A Catalytic Mechanism for D-Tyr-tRNATyr Deacylase Based on the Crystal Structure of Hemophilus influenzae HI0670 Authors: Lim, K. / Tempczyk, A. / Bonander, N. / Toedt, J. / Howard, A. / Einsenstein, E. / Herzberg, O. #1: Journal: J.Biol.Chem. / Year: 1999 Title: Functional Characterization of the D-Tyr-tRNA(Tyr) Deacylase from Escherichia coli Authors: Soutourina, J. / Plateau, P. / Delort, F. / Peirotes, A. / Blanquet, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j7g.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j7g.ent.gz | 30.9 KB | Display | PDB format |
PDBx/mmJSON format | 1j7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/1j7g ftp://data.pdbj.org/pub/pdb/validation_reports/j7/1j7g | 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: 15879.174 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria) Species: Haemophilus influenzae / Strain: Kw20 / Gene: HI0670 / Plasmid: pET15b-HI0670 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P44814, Hydrolases; Acting on ester bonds |
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#2: 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: 3.12 Å3/Da / Density % sol: 60.55 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K Method: crystal formed during dialysis of protein (2.8mg/ml) pH: 7.5 Details: 50 mM Tris, 0.1 mM DTT, 0.1 mM EDTA, pH 7.5, crystal formed during dialysis of protein (2.8mg/ml), temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→50 Å / Num. all: 25510 / Num. obs: 25510 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.64→1.71 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.135 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 352028 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: SAS / Resolution: 1.64→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 27 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.71 Å / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.238 | ||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.22 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.277 / Rfactor Rwork: 0.237 |