+Open data
-Basic information
Entry | Database: PDB / ID: 5no5 | ||||||
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Title | AbyA5 Wildtype | ||||||
Components | AbyA5 | ||||||
Keywords | HYDROLASE / Deacetylase / Elimination / Spirotetronate / Acetyl Lyase | ||||||
Function / homology | Esterase FrsA-like / Esterase FrsA-like / Alpha/Beta hydrolase fold / AbyA5 Function and homology information | ||||||
Biological species | Verrucosispora (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Byrne, M.J. / Race, P.R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2019 Title: An Esterase-like Lyase Catalyzes Acetate Elimination in Spirotetronate/Spirotetramate Biosynthesis. Authors: Lees, N.R. / Han, L.C. / Byrne, M.J. / Davies, J.A. / Parnell, A.E. / Moreland, P.E.J. / Stach, J.E.M. / van der Kamp, M.W. / Willis, C.L. / Race, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5no5.cif.gz | 141 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5no5.ent.gz | 111.2 KB | Display | PDB format |
PDBx/mmJSON format | 5no5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5no5_validation.pdf.gz | 447.1 KB | Display | wwPDB validaton report |
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Full document | 5no5_full_validation.pdf.gz | 451.9 KB | Display | |
Data in XML | 5no5_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 5no5_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/5no5 ftp://data.pdbj.org/pub/pdb/validation_reports/no/5no5 | HTTPS FTP |
-Related structure data
Related structure data | 4ywfSC 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
#1: Protein | Mass: 40776.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Verrucosispora (bacteria) / Gene: abyA5, VAB18032_16440 / Production host: Escherichia coli B (bacteria) / Variant (production host): B834 / References: UniProt: F4F7F5 #2: 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: 2.46 Å3/Da / Density % sol: 50.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Wild type AbyA5 data sets were collected from crystals formed in formed in 12.5 % w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M ...Details: Wild type AbyA5 data sets were collected from crystals formed in formed in 12.5 % w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine, HCl, 0.02 M DL-serine, 0.1 M Bicine/Trizma base pH 8.5 |
-Data collection
Diffraction | Mean temperature: 65 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97887 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97887 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→41.93 Å / Num. obs: 27564 / % possible obs: 96.6 % / Redundancy: 11.8 % / Net I/σ(I): 7.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YWF Resolution: 2.5→73.3 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.003 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.592 / ESU R Free: 0.306 / 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: 16.384 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→73.3 Å
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Refine LS restraints |
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