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Yorodumi- PDB-1hzj: HUMAN UDP-GALACTOSE 4-EPIMERASE: ACCOMMODATION OF UDP-N-ACETYLGLU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hzj | ||||||
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Title | HUMAN UDP-GALACTOSE 4-EPIMERASE: ACCOMMODATION OF UDP-N-ACETYLGLUCOSAMINE WITHIN THE ACTIVE SITE | ||||||
Components | UDP-GALACTOSE 4-EPIMERASE | ||||||
Keywords | ISOMERASE / Epimerase / Short-Chain Dehydrogenase / Galactosemia | ||||||
Function / homology | Function and homology information Defective GALE causes EDG / UDP-N-acetylglucosamine 4-epimerase / UDP-N-acetylglucosamine 4-epimerase activity / galactose catabolic process / Galactose catabolism / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Thoden, J.B. / Wohlers, T.M. / Fridovich-Keil, J.L. / Holden, H.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Human UDP-galactose 4-epimerase. Accommodation of UDP-N-acetylglucosamine within the active site. Authors: Thoden, J.B. / Wohlers, T.M. / Fridovich-Keil, J.L. / 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 | 1hzj.cif.gz | 174.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hzj.ent.gz | 134.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hzj_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 1hzj_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 1hzj_validation.xml.gz | 40.1 KB | Display | |
Data in CIF | 1hzj_validation.cif.gz | 61.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/1hzj ftp://data.pdbj.org/pub/pdb/validation_reports/hz/1hzj | HTTPS FTP |
-Related structure data
Related structure data | 1ek6S 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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Unit cell |
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Details | The biological assembly is a homodimer comprised of chains A and B in the crystallographic asymmetric unit. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38352.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPIC3.5KHGALE / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q14376, UDP-glucose 4-epimerase |
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-Non-polymers , 5 types, 939 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Chemical | #6: 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: 2.18 Å3/Da / Density % sol: 43.57 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 276 K / Method: batch / pH: 6 Details: PEG-3400, sodium chloride, magnesium chloride, MES, NADH, UDP-N-acetylglucosamine, pH 6.0, Batch, temperature 276K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: unknown / Details: used macroseeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Jun 24, 2000 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 104972 / Num. obs: 104972 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.9 / % possible all: 84.6 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 84.6 % / Num. unique obs: 8999 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1EK6 Resolution: 1.5→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Num. reflection obs: 96932 / σ(F): 0 / Rfactor all: 0.185 / Rfactor obs: 0.184 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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