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- PDB-1xru: Crystal Structure of 5-keto-4-deoxyuronate Isomerase from Escheri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xru | ||||||
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Title | Crystal Structure of 5-keto-4-deoxyuronate Isomerase from Eschericia coli | ||||||
![]() | 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase | ||||||
![]() | ISOMERASE / BETA BARREL / CUPIN | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Crowther, R.L. / Georgiadis, M.M. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.2 KB | Display | ![]() |
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PDB format | ![]() | 107.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.9 KB | Display | ![]() |
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Full document | ![]() | 456.2 KB | Display | |
Data in XML | ![]() | 26.9 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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. |
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Components
#1: Protein | Mass: 31874.428 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() | ||||||||||||
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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