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Yorodumi- PDB-3a9r: X-ray Structures of Bacillus pallidus D-Arabinose IsomeraseComple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a9r | ||||||
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Title | X-ray Structures of Bacillus pallidus D-Arabinose IsomeraseComplex with (4R)-2-METHYLPENTANE-2,4-DIOL | ||||||
Components | D-arabinose isomerase | ||||||
Keywords | ISOMERASE / ROSSMANN FOLD / BETA BARREL / Carbohydrate metabolism / Cytoplasm / Fucose metabolism / Manganese / Metal-binding | ||||||
Function / homology | Function and homology information arabinose isomerase activity / L-fucose isomerase / L-fucose isomerase activity / D-arabinose catabolic process / L-fucose catabolic process / manganese ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus pallidus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Takeda, K. / Yoshida, H. / Izumori, K. / Kamitori, S. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2010 Title: X-ray structures of Bacillus pallidusd-arabinose isomerase and its complex with l-fucitol. Authors: Takeda, K. / Yoshida, H. / Izumori, K. / Kamitori, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a9r.cif.gz | 370.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a9r.ent.gz | 298.4 KB | Display | PDB format |
PDBx/mmJSON format | 3a9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a9r_validation.pdf.gz | 463.4 KB | Display | wwPDB validaton report |
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Full document | 3a9r_full_validation.pdf.gz | 480 KB | Display | |
Data in XML | 3a9r_validation.xml.gz | 71.6 KB | Display | |
Data in CIF | 3a9r_validation.cif.gz | 104.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/3a9r ftp://data.pdbj.org/pub/pdb/validation_reports/a9/3a9r | HTTPS FTP |
-Related structure data
Related structure data | 3a9sC 3a9tC 1fuiS 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: 66220.047 Da / Num. of mol.: 3 / Mutation: E225G, N589K, F590L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus pallidus (bacteria) / Strain: 14a / Gene: dai / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: C0SSE7, D-arabinose isomerase #2: Chemical | #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: 2.58 Å3/Da / Density % sol: 52.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100mM citrate buffer pH 6.0, 20% (w/v) PEG 3000, 90mM potassium sodium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: May 15, 2009 |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. obs: 199894 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.77→1.8 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.8 / Num. unique all: 9753 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FUI Resolution: 1.77→41.83 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 135339.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.9339 Å2 / ksol: 0.327355 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.77→41.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.8 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 20
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Xplor file |
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