+Open data
-Basic information
Entry | Database: PDB / ID: 3fkk | ||||||
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Title | Structure of L-2-keto-3-deoxyarabonate dehydratase | ||||||
Components | L-2-keto-3-deoxyarabonate dehydratase | ||||||
Keywords | LYASE / DHDPS/NAL family | ||||||
Function / homology | Function and homology information 2-dehydro-3-deoxy-L-arabinonate dehydratase / 2-dehydro-3-deoxy-L-arabinonate dehydratase activity / L-arabinose catabolic process to 2-oxoglutarate / 4-hydroxy-tetrahydrodipicolinate synthase activity / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Azospirillum brasilense (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Shimada, N. / Mikami, B. | ||||||
Citation | Journal: To be Published Title: Structural analysis of L -2-keto-3-deoxyarabonate dehydratase an enzyme involved in an alternative bacterial pathway of L-arabinose metabolism in complex with pyruvate Authors: Shimada, N. / Mikami, B. / Watanabe, S. / Kodaki, T. / Makino, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fkk.cif.gz | 135.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fkk.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 3fkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fkk_validation.pdf.gz | 452 KB | Display | wwPDB validaton report |
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Full document | 3fkk_full_validation.pdf.gz | 463.9 KB | Display | |
Data in XML | 3fkk_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 3fkk_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/3fkk ftp://data.pdbj.org/pub/pdb/validation_reports/fk/3fkk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33781.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azospirillum brasilense (bacteria) / Gene: AraD / Production host: Escherichia coli (E. coli) / References: UniProt: Q1JUQ0 #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: 2.76 Å3/Da / Density % sol: 55.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50mM Tris-HCl,5% 2-propanol, 0.4M Ammonium phospate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
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Detector | Type: RIGAKU JUPITER 210 / Detector: CCD |
Radiation | Monochromator: Iodine / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.8 Å / Num. obs: 48899 / % possible obs: 94.6 % / Observed criterion σ(I): 29.2 / Biso Wilson estimate: 10.1 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→15 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4173414.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.5829 Å2 / ksol: 0.392056 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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