+Open data
-Basic information
Entry | Database: PDB / ID: 4gll | |||||||||
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Title | Crystal structure of human UDP-xylose synthase. | |||||||||
Components | UDP-glucuronic acid decarboxylase 1 | |||||||||
Keywords | LYASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / Decarboxylase / MEMBRANE | |||||||||
Function / homology | Function and homology information UDP-glucuronate decarboxylase / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / D-xylose metabolic process / Golgi cisterna membrane / catalytic complex / NAD+ binding / protein homodimerization activity / extracellular exosome / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Wood, Z.A. / Polizzi, S.J. | |||||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Human UDP-alpha-d-xylose Synthase and Escherichia coli ArnA Conserve a Conformational Shunt That Controls Whether Xylose or 4-Keto-Xylose Is Produced. Authors: Polizzi, S.J. / Walsh Jr., R.M. / Peeples, W.B. / Lim, J.M. / Wells, L. / Wood, Z.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gll.cif.gz | 136.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gll.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 4gll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/4gll ftp://data.pdbj.org/pub/pdb/validation_reports/gl/4gll | HTTPS FTP |
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-Related structure data
Related structure data | 2b69S 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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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 38055.371 Da / Num. of mol.: 2 / Fragment: Soluble UXS domain; residues 85-420 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UNQ2538/PRO6079, UXS, UXS1 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NBZ7, UDP-glucuronate decarboxylase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.96 Å3/Da / Density % sol: 58.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.3 M AMMONIUM SULFATE, 0.1 M MAGNESIUM FORMATE AND 0.15% 1.5K PEG, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2007 |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 31483 / Num. obs: 31483 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.5→2.57 Å / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2B69 Resolution: 2.5→45 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.67 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→45 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2376 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 20
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