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Yorodumi- PDB-7esl: Crystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7esl | ||||||
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Title | Crystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, N247A N-glycan free form | ||||||
Components | L-rhamnose-alpha-1,4-D-glucuronate lyase | ||||||
Keywords | LYASE / seven-bladed beta-propeller | ||||||
Biological species | Fusarium oxysporum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Kondo, T. / Arakawa, T. / Fushinobu, S. / Sakamoto, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Structural and functional analysis of gum arabic l-rhamnose-alpha-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family. Authors: Kondo, T. / Kichijo, M. / Maruta, A. / Nakaya, M. / Takenaka, S. / Arakawa, T. / Fushinobu, S. / Sakamoto, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7esl.cif.gz | 109.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7esl.ent.gz | 81.8 KB | Display | PDB format |
PDBx/mmJSON format | 7esl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7esl_validation.pdf.gz | 420.4 KB | Display | wwPDB validaton report |
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Full document | 7esl_full_validation.pdf.gz | 421.2 KB | Display | |
Data in XML | 7esl_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 7esl_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/7esl ftp://data.pdbj.org/pub/pdb/validation_reports/es/7esl | HTTPS FTP |
-Related 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: 50042.176 Da / Num. of mol.: 1 / Mutation: N247A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium oxysporum (fungus) / Strain: 12S / Gene: Forham1 / Plasmid: pPICZ-alpha-A / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 References: Lyases; Carbon-oxygen lyases; Acting on polysaccharides |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
Sequence details | The amino acid sequence of FoRham1 has been registered in GenBank, DDBj and EMBL. Its accession ...The amino acid sequence of FoRham1 has been registered in GenBank, DDBj and EMBL. Its accession number is LC617219. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.9 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30 % (v/v) PEG 1500, 0.1 M BICINE-NaOH (pH 8.5), 10 % (v/v) 2-propanol, Crystal was soaked into 20 % (v/v) glycerol at 298 K for 1 min |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 8, 2019 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 75319 / % possible obs: 94.2 % / Redundancy: 6.1 % / CC1/2: 1 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.4→1.42 Å / Num. unique obs: 2667 / CC1/2: 0.725 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→43.19 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.08 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.068 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.18 Å2 / Biso mean: 24.191 Å2 / Biso min: 13.55 Å2
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Refinement step | Cycle: final / Resolution: 1.4→43.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.401→1.437 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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