+Open data
-Basic information
Entry | Database: PDB / ID: 2wyl | ||||||
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Title | Apo structure of a metallo-b-lactamase | ||||||
Components | L-ASCORBATE-6-PHOSPHATE LACTONASE ULAG | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information L-ascorbate 6-phosphate lactonase activity / L-ascorbic acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / manganese ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å | ||||||
Authors | Garces, F. / Fernandez, F.J. / Penya-Soler, E. / Aguilar, J. / Baldoma, L. / Coll, M. / Badia, J. / Vega, M.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Molecular Architecture of the Mn(2+)Dependent Lactonase Ulag Reveals an Rnase-Like Metallo-Beta-Lactamase Fold and a Novel Quaternary Structure. Authors: Garces, F. / Fernandez, F.J. / Montella, C. / Penya-Soler, E. / Prohens, R. / Aguilar, J. / Baldoma, L. / Coll, M. / Badia, J. / Vega, M.C. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Overproduction, Crystallization and Preliminary X-Ray Analysis of the Putative L-Ascorbate-6-Phosphate Lactonase Ulag from Escherichia Coli. Authors: Garces, F. / Fernandez, F.J. / Perez-Luque, R. / Aguilar, J. / Baldoma, L. / Coll, M. / Badia, J. / Vega, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wyl.cif.gz | 363.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wyl.ent.gz | 310.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wyl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wyl_validation.pdf.gz | 497.3 KB | Display | wwPDB validaton report |
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Full document | 2wyl_full_validation.pdf.gz | 517.5 KB | Display | |
Data in XML | 2wyl_validation.xml.gz | 66.4 KB | Display | |
Data in CIF | 2wyl_validation.cif.gz | 88.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/2wyl ftp://data.pdbj.org/pub/pdb/validation_reports/wy/2wyl | 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
#1: Protein | Mass: 41454.289 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P39300, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % / Description: NONE |
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Crystal grow | Details: 20% PEG 3350, 200 MM LITHIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→24.79 Å / Num. obs: 60575 / % possible obs: 97.5 % / Observed criterion σ(I): 3 / Redundancy: 8.9 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.59→2.73 Å / Redundancy: 8.6 % / % possible all: 74 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.59→14.94 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.878 / SU B: 11.613 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.337 / 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: 30.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→14.94 Å
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Refine LS restraints |
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