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Yorodumi- PDB-4dqn: Crystal structure of the branched-chain aminotransferase from Str... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dqn | ||||||
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Title | Crystal structure of the branched-chain aminotransferase from Streptococcus mutans | ||||||
Components | Putative branched-chain amino acid aminotransferase IlvE | ||||||
Keywords | TRANSFERASE / aminotransferase | ||||||
Function / homology | Function and homology information 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 Similarity search - Function | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Ruan, J. / Li, S.T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structure of the branched-chain aminotransferase from Streptococcus mutans Authors: Ruan, J. / Hu, J. / Yin, A.H. / Wu, W.Q. / Cong, X.Z. / Feng, X.T. / Li, S.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dqn.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dqn.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 4dqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dqn_validation.pdf.gz | 423.8 KB | Display | wwPDB validaton report |
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Full document | 4dqn_full_validation.pdf.gz | 429.5 KB | Display | |
Data in XML | 4dqn_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 4dqn_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/4dqn ftp://data.pdbj.org/pub/pdb/validation_reports/dq/4dqn | HTTPS FTP |
-Related structure data
Related structure data | 3ht5S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 38053.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: ilvE, SMU_1203 / Production host: Escherichia coli (E. coli) References: UniProt: Q8DTW7, branched-chain-amino-acid transaminase |
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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: 2.62 Å3/Da / Density % sol: 53.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M sodium chloride, 100mM HEPES (pH 7.5), 25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. all: 29016 / Num. obs: 29016 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 31.28 Å2 |
Reflection shell | Resolution: 1.97→2.01 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HT5 Resolution: 1.97→34.067 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 21.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.453 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→34.067 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %
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