+Open data
-Basic information
Entry | Database: PDB / ID: 6ibu | ||||||
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Title | Apo Crh5 transglycosylase | ||||||
Components | Probable glycosidase crf1 | ||||||
Keywords | HYDROLASE / cross-link / transglycosylase / GH16 / cell wall assembly | ||||||
Function / homology | Function and homology information Hydrolases; Glycosylases / fungal-type cell wall / IgE binding / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / carbohydrate metabolic process / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Neosartorya fumigata (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Bartual, S.G. / Fang, W. / van Aalten, D.M.F. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Mechanisms of redundancy and specificity of the Aspergillus fumigatus Crh transglycosylases. Authors: Fang, W. / Sanz, A.B. / Bartual, S.G. / Wang, B. / Ferenbach, A.T. / Farkas, V. / Hurtado-Guerrero, R. / Arroyo, J. / van Aalten, D.M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ibu.cif.gz | 111.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ibu.ent.gz | 84.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ibu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ibu_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 6ibu_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 6ibu_validation.xml.gz | 22 KB | Display | |
Data in CIF | 6ibu_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/6ibu ftp://data.pdbj.org/pub/pdb/validation_reports/ib/6ibu | HTTPS FTP |
-Related structure data
Related structure data | 6ibwC 5ndl C: citing same article (ref.) 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 25 - 266 / Label seq-ID: 4 - 245
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-Components
#1: Protein | Mass: 26597.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold) Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: crf1, AFUA_1G16190 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8J0P4, Hydrolases; Glycosylases #2: Chemical | ChemComp-GOL / #3: 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: 2.26 Å3/Da / Density % sol: 45.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium acetate trihydrate pH 4.0, 1,6M ammonium sulphate, 21mM ZnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.885601 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.885601 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→62.62 Å / Num. obs: 23428 / % possible obs: 99.01 % / Redundancy: 4.1 % / CC1/2: 0.807 / Net I/σ(I): 7.99 |
Reflection shell | Resolution: 2.25→2.331 Å / Redundancy: 4.2 % / Num. unique obs: 2317 / % possible all: 99.44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NDL 5ndl Resolution: 2.25→62.62 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.582 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.224 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.229 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→62.62 Å
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Refine LS restraints |
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