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Yorodumi- PDB-2q1c: 2-keto-3-deoxy-D-arabinonate dehydratase complexed with calcium a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q1c | |||||||||
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Title | 2-keto-3-deoxy-D-arabinonate dehydratase complexed with calcium and 2-oxobutyrate | |||||||||
Components | 2-keto-3-deoxy-D-arabinonate dehydratase | |||||||||
Keywords | LYASE / FAH-family fold | |||||||||
Function / homology | Function and homology information 2-dehydro-3-deoxy-D-arabinonate dehydratase / D-arabinose catabolic process / hydro-lyase activity / protein homotetramerization / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Sulfolobus solfataricus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å | |||||||||
Authors | Barends, T. / Brouns, S. / Worm, P. / Akerboom, J. / Turnbull, A. / Salmon, L. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily. Authors: Brouns, S.J. / Barends, T.R. / Worm, P. / Akerboom, J. / Turnbull, A.P. / Salmon, L. / van der Oost, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q1c.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q1c.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 2q1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/2q1c ftp://data.pdbj.org/pub/pdb/validation_reports/q1/2q1c | HTTPS FTP |
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-Related structure data
Related structure data | 2q18C 2q19C 2q1aC 2q1dC 3bqbC 1q18S 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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Details | The biological assembly is a tetramer. A tetramer can be generated with the crystallographic symmetry operators. |
-Components
#1: Protein | Mass: 33185.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: kdaD / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q97UA0 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-2KT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: Na/K phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2006 / Details: osmic mirrors |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→19.5 Å / Num. all: 22992 / Num. obs: 22992 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1Q18 Resolution: 2.8→19.48 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.875 / SU B: 10.611 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.833 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
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