+Open data
-Basic information
Entry | Database: PDB / ID: 2q6v | ||||||
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Title | Crystal Structure of GumK in complex with UDP | ||||||
Components | Glucuronosyltransferase GumK | ||||||
Keywords | TRANSFERASE / Glucuronosyltransferase / glycosyltransferase / xanthan / Xanthomonas campestris / UDP / UDPGlcA | ||||||
Function / homology | Function and homology information D-Man-alpha-(1->3)-D-Glc-beta-(1->4)-D-Glc-alpha-1-diphosphoundecaprenol 2-beta-glucuronosyltransferase / glucuronosyltransferase activity / polysaccharide biosynthetic process / plasma membrane Similarity search - Function | ||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / ARP/wARP / Resolution: 2.28 Å | ||||||
Authors | Barreras, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structure and mechanism of GumK, a membrane-associated glucuronosyltransferase. Authors: Barreras, M. / Salinas, S.R. / Abdian, P.L. / Kampel, M.A. / Ielpi, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q6v.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q6v.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 2q6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q6v_validation.pdf.gz | 836.2 KB | Display | wwPDB validaton report |
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Full document | 2q6v_full_validation.pdf.gz | 843.5 KB | Display | |
Data in XML | 2q6v_validation.xml.gz | 21 KB | Display | |
Data in CIF | 2q6v_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/2q6v ftp://data.pdbj.org/pub/pdb/validation_reports/q6/2q6v | HTTPS FTP |
-Related structure data
Related structure data | 2hy7SC 3cuyC 3cv3C S: Starting model for refinement C: citing same article (ref.) |
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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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45335.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria) Gene: gumK / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GCH2, glucuronosyltransferase |
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#2: Chemical | ChemComp-UDP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.99 Å3/Da / Density % sol: 69.19 % |
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Crystal grow | Temperature: 293 K / Method: hanging drop, soaking of crystals in udpglca 100 mm / pH: 8.2 Details: 0.1 M Tris-HCl, 35% (w/v) PEG 3350, 0.2 M Li2SO4, 0.1 M LiCl, pH 8.2, hanging drop and soaking of crystals in UDPGlcA 100 mM, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.427 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 13, 2006 / Details: beam focused by a cilindrically curved mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Silicium curved crystal, with asymmetric 7.25 angle cut Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.427 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.28→104.971 Å / Num. obs: 33916 / % possible obs: 98.5 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 4.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: ARP/wARP Starting model: PDB entry 2HY7 Apo protein GumK Resolution: 2.28→104.83 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.644 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 21.077 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→104.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.339 Å / Total num. of bins used: 20
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