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Yorodumi- PDB-2i5q: Crystal structure of Apo L-rhamnonate dehydratase from Escherichi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i5q | ||||||
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Title | Crystal structure of Apo L-rhamnonate dehydratase from Escherichia Coli | ||||||
Components | L-rhamnonate dehydratase | ||||||
Keywords | LYASE / Enolase superfamily / Clone name 9265b1BCt1p1_10997_1 / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information L-rhamnonate dehydratase / L-rhamnonate dehydratase activity / amino acid catabolic process / hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Sauder, J.M. / Burley, S.K. / Gerlt, J.A. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. Authors: Rakus, J.F. / Fedorov, A.A. / Fedorov, E.V. / Glasner, M.E. / Hubbard, B.K. / Delli, J.D. / Babbitt, P.C. / Almo, S.C. / Gerlt, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i5q.cif.gz | 157.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i5q.ent.gz | 124.1 KB | Display | PDB format |
PDBx/mmJSON format | 2i5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i5q_validation.pdf.gz | 409.9 KB | Display | wwPDB validaton report |
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Full document | 2i5q_full_validation.pdf.gz | 420.3 KB | Display | |
Data in XML | 2i5q_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 2i5q_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/2i5q ftp://data.pdbj.org/pub/pdb/validation_reports/i5/2i5q | HTTPS FTP |
-Related structure data
Related structure data | 3boxC 3cxoC 1rvkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | The biological assembly is the dimer AB |
-Components
#1: Protein | Mass: 46003.277 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XE07, UniProt: P77215*PLUS #2: 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: 2.2 Å3/Da / Density % sol: 43.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.2 M ammonium sulfate, 0.1M Tris-HCl, 0.2 M Lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97911 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 3, 2006 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. all: 44477 / Num. obs: 44477 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.5 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RVK Resolution: 2.1→24.89 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 132130.71 / 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: 46.336 Å2 / ksol: 0.388889 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→24.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
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Xplor file |
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