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Yorodumi- PDB-1xru: Crystal Structure of 5-keto-4-deoxyuronate Isomerase from Escheri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xru | ||||||
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Title | Crystal Structure of 5-keto-4-deoxyuronate Isomerase from Eschericia coli | ||||||
Components | 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase | ||||||
Keywords | ISOMERASE / BETA BARREL / CUPIN | ||||||
Function / homology | Function and homology information 5-dehydro-4-deoxy-D-glucuronate isomerase / 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity / D-galacturonate catabolic process / D-glucuronate catabolic process / glucose-6-phosphate isomerase activity / pectin catabolic process / protein homodimerization activity / zinc ion binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å | ||||||
Authors | Crowther, R.L. / Georgiadis, M.M. | ||||||
Citation | Journal: Proteins / Year: 2005 Title: The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli Authors: Crowther, R.L. / Georgiadis, M.M. | ||||||
History |
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Remark 999 | SEQUENCE Author states that the C-terminal differences from database sequence is a neutral ...SEQUENCE Author states that the C-terminal differences from database sequence is a neutral designation. The C-terminal sequence reported here is indeed correct for the gene that was cloned and for protein that was crystallized. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xru.cif.gz | 129.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xru.ent.gz | 107.1 KB | Display | PDB format |
PDBx/mmJSON format | 1xru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xru_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 1xru_full_validation.pdf.gz | 456.2 KB | Display | |
Data in XML | 1xru_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 1xru_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/1xru ftp://data.pdbj.org/pub/pdb/validation_reports/xr/1xru | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 hexamer generated from the dimer in the asymmetric unit by the operations: -y, x-y, z and y-x, -x, z. |
-Components
#1: Protein | Mass: 31874.428 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kduI / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): B834 References: UniProt: Q46938, 5-dehydro-4-deoxy-D-glucuronate isomerase #2: Chemical | #3: Chemical | #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: 2.9 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 Details: PEG 400, calcium chloride, HEPES, pH 7, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.980122, 0.979634, 0.979538 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2002 | ||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.94→50 Å / Num. all: 51624 / Num. obs: 51573 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rsym value: 0.07 / Net I/σ(I): 9 | ||||||||||||
Reflection shell | Resolution: 1.94→2.01 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 5124 / Rsym value: 0.2 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.94→12.97 Å / Isotropic thermal model: OVERALL / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 16.6 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.2 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→12.97 Å
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Refine LS restraints |
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