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Yorodumi- PDB-1a9z: UDP-GALACTOSE 4-EPIMERASE MUTANT S124A/Y149F COMPLEXED WITH UDP-G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a9z | |||||||||
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Title | UDP-GALACTOSE 4-EPIMERASE MUTANT S124A/Y149F COMPLEXED WITH UDP-GALACTOSE | |||||||||
Components | UDP-GALACTOSE 4-EPIMERASE | |||||||||
Keywords | EPIMERASE / GALACTOSE METABOLISM / DEHYDROGENASE | |||||||||
Function / homology | Function and homology information colanic acid biosynthetic process / racemase and epimerase activity, acting on carbohydrates and derivatives / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose / galactose metabolic process / NAD+ binding / carbohydrate metabolic process / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER DIFFERENCE / Resolution: 1.9 Å | |||||||||
Authors | Thoden, J.B. / Holden, H.M. | |||||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Dramatic differences in the binding of UDP-galactose and UDP-glucose to UDP-galactose 4-epimerase from Escherichia coli. Authors: Thoden, J.B. / Holden, H.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a9z.cif.gz | 98.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a9z.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 1a9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a9z_validation.pdf.gz | 547.6 KB | Display | wwPDB validaton report |
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Full document | 1a9z_full_validation.pdf.gz | 563.7 KB | Display | |
Data in XML | 1a9z_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1a9z_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/1a9z ftp://data.pdbj.org/pub/pdb/validation_reports/a9/1a9z | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37262.016 Da / Num. of mol.: 1 / Mutation: S124A, Y149F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P09147, UDP-glucose 4-epimerase |
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-Non-polymers , 5 types, 547 molecules
#2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-UPG / | #5: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | NAD IS THE COFACTOR UDP IS THE SUBSTRATE |
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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: 3 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 9 Details: CRYSTALLIZED FROM 18% PEG8000, 500MM NACL, 20MM UDP-GALACTOSE THEN SOAKED IN 25% PEG8000, 750MM NACL, 20MM UDP-GALACTOSE, 20% ETHYLENE GLYCOL, pH 9.0 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Mar 1, 1998 / Details: GOEBEL FOCUSING OPTICS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 32710 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.9→1.99 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.228 / % possible all: 74 |
Reflection | *PLUS Num. measured all: 112562 |
Reflection shell | *PLUS % possible obs: 74 % / Num. unique obs: 3288 / Num. measured obs: 5712 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER DIFFERENCE / Resolution: 1.9→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: TNT / Bsol: 906.6 Å2 / ksol: 1.236 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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