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Yorodumi- PDB-3dyi: Snapshots of esterase D from lactobacillus rhamnosus: Insights in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dyi | ||||||
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Title | Snapshots of esterase D from lactobacillus rhamnosus: Insights into a rotation driven catalytic mechanism | ||||||
Components | Esterase D | ||||||
Keywords | HYDROLASE / alpha beta hydrolase / catalytic triad / rotation / esterase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus rhamnosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å | ||||||
Authors | Bennett, M.D. / Delabre, M.-L. / Holland, R. / Norris, G.E. | ||||||
Citation | Journal: To be Published Title: Snapshots of esterase D from lactobacillus rhamnosus: Insights into a rotation driven catalytic mechanism Authors: Bennett, M.D. / Delabre, M.-L. / Holland, R. / Norris, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dyi.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dyi.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 3dyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dyi_validation.pdf.gz | 419.9 KB | Display | wwPDB validaton report |
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Full document | 3dyi_full_validation.pdf.gz | 420.9 KB | Display | |
Data in XML | 3dyi_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 3dyi_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/3dyi ftp://data.pdbj.org/pub/pdb/validation_reports/dy/3dyi | HTTPS FTP |
-Related structure data
Related structure data | 3dltC 3dyvC 3e1gC 3dkrS 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: 27327.963 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) / Strain: HN001 / Gene: EstD / Plasmid: pPROEXHT C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2CZF3 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.6 % |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 6 Details: PEG 8000, Na acetate, pH 6.0, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 8, 2006 / Details: Osmic Blue |
Radiation | Monochromator: Osmic Blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→33.54 Å / Num. all: 31093 / Num. obs: 29366 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DKR Resolution: 1.72→33.54 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.867 / SU B: 1.97 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.108 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 46.27 Å2 / Biso mean: 25.404 Å2 / Biso min: 18.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→33.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.765 Å / Total num. of bins used: 20
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