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Yorodumi- PDB-6tj2: Extracellular alpha/beta-hydrolase from Paenibacillus species sha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tj2 | |||||||||
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Title | Extracellular alpha/beta-hydrolase from Paenibacillus species shares structural and functional homology to Tobacco Salicylic Acid Binding Protein 2 | |||||||||
Components | Alpha/beta hydrolase | |||||||||
Keywords | HYDROLASE / alpha/beta-hydrolase / methyl salicylate esterase / Paenibacillus / rhizosphere / SABP2 / salicylic acid | |||||||||
Function / homology | Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Alpha/beta hydrolase Function and homology information | |||||||||
Biological species | Paenibacillus sp. VTT E-133280 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | |||||||||
Authors | Fulop, V. / Wilkinson, R.C. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: J.Struct.Biol. / Year: 2020 Title: Extracellular alpha/beta-hydrolase from Paenibacillus species shares structural and functional homology to tobacco salicylic acid binding protein 2. Authors: Wilkinson, R.C. / Rahman Pour, R. / Jamshidi, S. / Fulop, V. / Bugg, T.D.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tj2.cif.gz | 167.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tj2.ent.gz | 130.7 KB | Display | PDB format |
PDBx/mmJSON format | 6tj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tj2_validation.pdf.gz | 430.6 KB | Display | wwPDB validaton report |
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Full document | 6tj2_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 6tj2_validation.xml.gz | 33 KB | Display | |
Data in CIF | 6tj2_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/6tj2 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/6tj2 | HTTPS FTP |
-Related structure data
Related structure data | 3dqzS S: Starting model for refinement |
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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: 31771.234 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus sp. VTT E-133280 (bacteria) Gene: CA600_10415 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A264DUQ2 #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: 1.79 Å3/Da / Density % sol: 31.3 % / Description: Rod |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium fluoride, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2017 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→57 Å / Num. obs: 159905 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 15.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Rrim(I) all: 0.064 / Rsym value: 0.059 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.32→1.39 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 2 / Num. unique obs: 22076 / CC1/2: 0.737 / Rpim(I) all: 0.32 / Rrim(I) all: 0.807 / Rsym value: 0.739 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DQZ Resolution: 1.32→56.22 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.824 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.05 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.83 Å2 / Biso mean: 15.128 Å2 / Biso min: 8.63 Å2
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Refinement step | Cycle: final / Resolution: 1.32→56.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.32→1.354 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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