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Yorodumi- PDB-2qun: Crystal Structure of D-tagatose 3-epimerase from Pseudomonas cich... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qun | ||||||
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Title | Crystal Structure of D-tagatose 3-epimerase from Pseudomonas cichorii in Complex with D-fructose | ||||||
Components | D-tagatose 3-epimerase | ||||||
Keywords | ISOMERASE / BETA/ALPHA BARREL | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas cichorii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Yoshida, H. / Yamada, M. / Nishitani, T. / Takada, G. / Izumori, K. / Kamitori, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal structures of D-tagatose 3-epimerase from Pseudomonas cichorii and its complexes with D-tagatose and D-fructose Authors: Yoshida, H. / Yamada, M. / Nishitani, T. / Takada, G. / Izumori, K. / Kamitori, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qun.cif.gz | 252.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qun.ent.gz | 201.3 KB | Display | PDB format |
PDBx/mmJSON format | 2qun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qun_validation.pdf.gz | 472.1 KB | Display | wwPDB validaton report |
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Full document | 2qun_full_validation.pdf.gz | 490.4 KB | Display | |
Data in XML | 2qun_validation.xml.gz | 53.6 KB | Display | |
Data in CIF | 2qun_validation.cif.gz | 76.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/2qun ftp://data.pdbj.org/pub/pdb/validation_reports/qu/2qun | HTTPS FTP |
-Related structure data
Related structure data | 2ou4SC 2qulC 2qumC 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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-Components
#1: Protein | Mass: 32657.404 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas cichorii (bacteria) / Strain: ST-24 / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: O50580, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds #2: Sugar | ChemComp-FUD / #3: Chemical | ChemComp-MN / #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: 2.35 Å3/Da / Density % sol: 47.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 10000, 0.1M HEPES, 0.1M tri-sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2007 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. all: 74020 / Num. obs: 74020 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.06→2.13 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 10.3 / Num. unique all: 7369 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OU4 Resolution: 2.06→47.3 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 68760.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.8174 Å2 / ksol: 0.391226 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.06→47.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.19 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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