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Yorodumi- PDB-3ito: Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ito | ||||||
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Title | Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant D327N in complex with D-psicose | ||||||
Components | L-rhamnose isomerase | ||||||
Keywords | ISOMERASE / METAL-BINDING PROTEIN / BETA/ALPHA BARREL / HOMO-TETRAMER / TIM barrel | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas stutzeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Yoshida, H. / Yamaji, M. / Ishii, T. / Izumori, K. / Kamitori, S. | ||||||
Citation | Journal: Febs J. / Year: 2010 Title: Catalytic reaction mechanism of Pseudomonas stutzeri l-rhamnose isomerase deduced from X-ray structures Authors: Yoshida, H. / Yamaji, M. / Ishii, T. / Izumori, K. / Kamitori, S. #1: Journal: J.Mol.Biol. / Year: 2007 Title: The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity Authors: Yoshida, H. / Yamada, M. / Ohyama, Y. / 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 | 3ito.cif.gz | 360.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ito.ent.gz | 289.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ito.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ito_validation.pdf.gz | 477.4 KB | Display | wwPDB validaton report |
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Full document | 3ito_full_validation.pdf.gz | 493.4 KB | Display | |
Data in XML | 3ito_validation.xml.gz | 72.9 KB | Display | |
Data in CIF | 3ito_validation.cif.gz | 106.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/3ito ftp://data.pdbj.org/pub/pdb/validation_reports/it/3ito | HTTPS FTP |
-Related structure data
Related structure data | 3itlC 3ittC 3itvC 3itxC 3ityC 3iudC 3iuhC 3iuiC 2hcvS S: Starting model for refinement C: citing same article (ref.) |
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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: 48003.629 Da / Num. of mol.: 4 / Mutation: D150N, D327N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q75WH8, L-rhamnose isomerase #2: Chemical | ChemComp-MN / #3: Sugar | ChemComp-PSV / #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: 2.23 Å3/Da / Density % sol: 44.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 7-8% (W/V) polyethylene glycol 20000, 50mM MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 5, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 128987 / Num. obs: 128987 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 3.4 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HCV Resolution: 1.9→42.15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 28752.31 / 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: 48.5804 Å2 / ksol: 0.379471 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→42.15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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