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Yorodumi- PDB-5byu: Crystal structure of unnamed thioesterase Ipg2867 from Legionella... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5byu | ||||||
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Title | Crystal structure of unnamed thioesterase Ipg2867 from Legionella pneumophila | ||||||
Components | Thioesterase | ||||||
Keywords | HYDROLASE / Thioesterase / hotdog fold / 4HBT | ||||||
Function / homology | Thioesterase-like superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / COENZYME A / Thioesterase Function and homology information | ||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Swarbrick, C.M.D. / Forwood, J.K. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of unnamed thioesterase Ipg2867 from Legionella pneumophila Authors: Swarbrick, C.M.D. / Forwood, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5byu.cif.gz | 211.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5byu.ent.gz | 170.3 KB | Display | PDB format |
PDBx/mmJSON format | 5byu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5byu_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5byu_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5byu_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 5byu_validation.cif.gz | 54.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/5byu ftp://data.pdbj.org/pub/pdb/validation_reports/by/5byu | HTTPS FTP |
-Related structure data
Related structure data | 3qy3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15183.446 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2867 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 pLysS / References: UniProt: Q5ZRL4 #2: Chemical | ChemComp-COA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.57 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 40 mM citric acid, 30 mM bis-tris propane, 14% PEG 3350 and 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→35 Å / Num. obs: 40946 / % possible obs: 96.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 4.5 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QY3 Resolution: 2.4→34.998 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.57 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→34.998 Å
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Refine LS restraints |
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LS refinement shell |
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