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Yorodumi- PDB-7v1w: Difructose dianhydride I synthase/hydrolase (alphaFFase1) from Bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v1w | |||||||||
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Title | Difructose dianhydride I synthase/hydrolase (alphaFFase1) from Bifidobacterium dentium in complex with beta-D-arabinofuranose | |||||||||
Components | Difructose dianhydride I synthase/hydrolase (alphaFFase1) | |||||||||
Keywords | HYDROLASE / Glycoside Hydrolase / alpha-D-fructofuranosidase / beta-D-arabinofuranose complex | |||||||||
Function / homology | Protein of unknown function DUF2961 / Protein of unknown function (DUF2961) / metal ion binding / beta-D-arabinofuranose / DUF2961 domain-containing protein Function and homology information | |||||||||
Biological species | Bifidobacterium dentium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | |||||||||
Authors | Kashima, T. / Arakawa, T. / Yamada, C. / Fujita, K. / Fushinobu, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family. Authors: Kashima, T. / Okumura, K. / Ishiwata, A. / Kaieda, M. / Terada, T. / Arakawa, T. / Yamada, C. / Shimizu, K. / Tanaka, K. / Kitaoka, M. / Ito, Y. / Fujita, K. / Fushinobu, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v1w.cif.gz | 571.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v1w.ent.gz | 465.6 KB | Display | PDB format |
PDBx/mmJSON format | 7v1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v1w_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 7v1w_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7v1w_validation.xml.gz | 105.5 KB | Display | |
Data in CIF | 7v1w_validation.cif.gz | 155.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/7v1w ftp://data.pdbj.org/pub/pdb/validation_reports/v1/7v1w | HTTPS FTP |
-Related structure data
Related structure data | 7v1vC 7v1xC 4kq7S 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: 53045.027 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium dentium (bacteria) / Gene: BDLFYP24_02130 / Plasmid: pET23d / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6L9SN29 #2: Chemical | ChemComp-CA / #3: Sugar | ChemComp-BXX / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.36 Å3/Da / Density % sol: 47.95 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M di-sodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2019 |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→48.77 Å / Num. obs: 237104 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.05 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.05 / Rrim(I) all: 0.132 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.87→1.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 11654 / CC1/2: 0.811 / Rpim(I) all: 0.489 / Rrim(I) all: 0.912 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KQ7 Resolution: 1.86→48.77 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.587 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.33 Å2 / Biso mean: 27.033 Å2 / Biso min: 15.02 Å2
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Refinement step | Cycle: final / Resolution: 1.86→48.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.865→1.913 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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