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Open data
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Basic information
Entry | Database: PDB / ID: 2wym | ||||||
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Title | Structure of a metallo-b-lactamase | ||||||
![]() | (L-ASCORBATE-6-PHOSPHATE LACTONASE ...) x 2 | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garces, F. / Fernandez, F.J. / Penya-Soler, E. / Aguilar, J. / Baldoma, L. / Coll, M. / Badia, J. / Vega, M.C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 361.3 KB | Display | ![]() |
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PDB format | ![]() | 294.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 511.2 KB | Display | ![]() |
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Full document | ![]() | 528.8 KB | Display | |
Data in XML | ![]() | 63.7 KB | Display | |
Data in CIF | ![]() | 85.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wylSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-L-ASCORBATE-6-PHOSPHATE LACTONASE ... , 2 types, 6 molecules ABDECF
#1: Protein | Mass: 40938.445 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P39300, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases #2: Protein | Mass: 40966.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P39300, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
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-Non-polymers , 4 types, 207 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-FLC / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.6 % / Description: NONE |
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Crystal grow | Details: 20% PEG 3350, 0.2M LITHIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→24.5 Å / Num. obs: 60423 / % possible obs: 91.5 % / Observed criterion σ(I): 8.3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 3.19 / % possible all: 70.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WYL Resolution: 2.6→14.97 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.886 / SU B: 13.482 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R Free: 0.344 / 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: 40.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→14.97 Å
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Refine LS restraints |
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