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Yorodumi- PDB-3o05: Crystal Structure of Yeast Pyridoxal 5-Phosphate Synthase Snz1 Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o05 | ||||||
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Title | Crystal Structure of Yeast Pyridoxal 5-Phosphate Synthase Snz1 Complxed with Substrate PLP | ||||||
Components | Pyridoxine biosynthesis protein SNZ1 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / beta slash alpha barrel / (beat/alpha)8-barrel / pyridoxal 5-phosphate synthase / PLP G3P RBP Sno1 | ||||||
Function / homology | Function and homology information vitamin B6 biosynthetic process / glutaminase complex / amine-lyase activity / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / glutamine catabolic process / pyridoxine biosynthetic process / amino acid metabolic process Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å | ||||||
Authors | Teng, Y.B. / Zhang, X. / He, Y.X. / Hu, H.X. / Zhou, C.Z. | ||||||
Citation | Journal: Biochem.J. / Year: 2010 Title: Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1 Authors: Zhang, X. / Teng, Y.B. / Liu, J.P. / He, Y.X. / Zhou, K. / Chen, Y. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o05.cif.gz | 164.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o05.ent.gz | 129.8 KB | Display | PDB format |
PDBx/mmJSON format | 3o05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/3o05 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/3o05 | HTTPS FTP |
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-Related structure data
Related structure data | 3o06C 3o07C 1znnS 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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Unit cell |
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-Components
#1: Protein | Mass: 31366.279 Da / Num. of mol.: 3 / Fragment: residues 15-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SNZ1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: Q03148 #2: Chemical | #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: 2.66 Å3/Da / Density % sol: 53.83 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 400, 0.1M Megnesium Cloride, 0.1M HEPES, 2.5mM PLP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→32.4 Å / Num. all: 51330 / Num. obs: 51330 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.2→2.24 Å / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: 1znn Resolution: 2.2→32.4 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.336 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→32.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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