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Yorodumi- PDB-7jqx: Crystal structure of Cfl1 wild-type from Burkholderia cenocepacia -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jqx | |||||||||||||||||||||
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Title | Crystal structure of Cfl1 wild-type from Burkholderia cenocepacia | |||||||||||||||||||||
Components | Cif-like 1 wild-type | |||||||||||||||||||||
Keywords | HYDROLASE / Octamer / alpha/beta hydrolase fold | |||||||||||||||||||||
Function / homology | Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Putative hydrolase Function and homology information | |||||||||||||||||||||
Biological species | Burkholderia cenocepacia (bacteria) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||||||||||||||
Authors | Taher, N.M. / Madden, D.R. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Curr Res Struct Biol / Year: 2021 Title: Biochemical and structural characterization of two cif-like epoxide hydrolases from Burkholderia cenocepacia . Authors: Taher, N.M. / Hvorecny, K.L. / Burke, C.M. / Gilman, M.S.A. / Heussler, G.E. / Adolf-Bryfogle, J. / Bahl, C.D. / O'Toole, G.A. / Madden, D.R. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jqx.cif.gz | 247.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jqx.ent.gz | 199.2 KB | Display | PDB format |
PDBx/mmJSON format | 7jqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/7jqx ftp://data.pdbj.org/pub/pdb/validation_reports/jq/7jqx | HTTPS FTP |
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-Related structure data
Related structure data | 7jqyC 7jqzC 3kd2S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 11 - 304 / Label seq-ID: 11 - 304
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-Components
#1: Protein | Mass: 34539.324 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria) Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610 Gene: BCAM1529 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EJL9 #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: 2.84 Å3/Da / Density % sol: 56.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 750 mM potassium sodium tartrate, 100 mM HEPES pH 8.1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.63 Å / Num. obs: 76696 / % possible obs: 99.5 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rrim(I) all: 0.178 / Net I/σ(I): 11.71 |
Reflection shell | Resolution: 2.2→2.33 Å / Num. unique obs: 11911 / CC1/2: 0.794 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KD2 Resolution: 2.2→48.63 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.92 Å2 / Biso mean: 42.2694 Å2 / Biso min: 24.56 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→48.63 Å
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Refine LS restraints NCS |
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