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Yorodumi- PDB-3k4d: Crystal structure of E. coli beta-glucuronidase with the glucaro-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k4d | ||||||
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Title | Crystal structure of E. coli beta-glucuronidase with the glucaro-d-lactam inhibitor bound | ||||||
Components | Beta-glucuronidase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / alpha/beta barrel / sugar-binding domain / beta-sandwich domain / glycosyl hydrolase / glucaro-d-lactam / Glycosidase / Hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / carbohydrate binding / carbohydrate metabolic process / signaling receptor binding / protein-containing complex / extracellular space / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.393 Å | ||||||
Authors | Wallace, B.D. / Redinbo, M.R. | ||||||
Citation | Journal: Science / Year: 2010 Title: Alleviating cancer drug toxicity by inhibiting a bacterial enzyme. Authors: Wallace, B.D. / Wang, H. / Lane, K.T. / Scott, J.E. / Orans, J. / Koo, J.S. / Venkatesh, M. / Jobin, C. / Yeh, L.A. / Mani, S. / Redinbo, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k4d.cif.gz | 502 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k4d.ent.gz | 417.9 KB | Display | PDB format |
PDBx/mmJSON format | 3k4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k4d_validation.pdf.gz | 473.8 KB | Display | wwPDB validaton report |
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Full document | 3k4d_full_validation.pdf.gz | 551.4 KB | Display | |
Data in XML | 3k4d_validation.xml.gz | 57 KB | Display | |
Data in CIF | 3k4d_validation.cif.gz | 78.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/3k4d ftp://data.pdbj.org/pub/pdb/validation_reports/k4/3k4d | HTTPS FTP |
-Related structure data
Related structure data | 3k46C 3k4aSC 3lpfC 3lpgC C: citing same article (ref.) 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 68746.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1617, gurA, gusA, JW1609, uidA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05804, beta-glucuronidase #2: Chemical | #3: 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: 2.41 Å3/Da / Density % sol: 49.01 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 15% PEG 3350, 0.2 M Mg Acetate, 0.02% Sodium azide, 500 mM Glucaro-d-lactam, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.393→50 Å / Num. obs: 51884 / % possible obs: 98.33 % / Redundancy: 7 % / Rmerge(I) obs: 0.082 |
Reflection shell | Resolution: 2.393→2.49 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.422 / % possible all: 93.9 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3K4A Resolution: 2.393→29.57 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / SU B: 19.42 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R Free: 0.262 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.393→29.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.393→2.455 Å / Total num. of bins used: 20
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