+Open data
-Basic information
Entry | Database: PDB / ID: 7osk | ||||||
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Title | Ignisphaera aggregans GH53 catalytic domain | ||||||
Components | Arabinogalactan endo-1,4-beta-galactosidase | ||||||
Keywords | HYDROLASE / galactanase / thermostable | ||||||
Function / homology | Function and homology information arabinogalactan endo-beta-1,4-galactanase / arabinogalactan endo-1,4-beta-galactosidase activity / glucosidase activity / metabolic process / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Ignisphaera aggregans (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Fredslund, F. / Lo Leggio, L. / Poulsen, J.C. / Rasmussen, K.K. / Muderspach, S. / Krogh, K.B.R.M. / Jensen, K. | ||||||
Citation | Journal: Biotechnol Biofuels / Year: 2021 Title: Engineering the substrate binding site of the hyperthermostable archaeal endo-beta-1,4-galactanase from Ignisphaera aggregans. Authors: Muderspach, S.J. / Fredslund, F. / Volf, V. / Poulsen, J.N. / Blicher, T.H. / Clausen, M.H. / Rasmussen, K.K. / Krogh, K.B.R.M. / Jensen, K. / Lo Leggio, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7osk.cif.gz | 277.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7osk.ent.gz | 224.2 KB | Display | PDB format |
PDBx/mmJSON format | 7osk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7osk_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 7osk_full_validation.pdf.gz | 446.2 KB | Display | |
Data in XML | 7osk_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 7osk_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/7osk ftp://data.pdbj.org/pub/pdb/validation_reports/os/7osk | HTTPS FTP |
-Related structure data
Related structure data | 1ur4S 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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-Components
#1: Protein | Mass: 45990.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ignisphaera aggregans (strain DSM 17230 / JCM 13409 / AQ1.S1) (archaea) Strain: DSM 17230 / JCM 13409 / AQ1.S1 / Gene: Igag_0688 / Production host: Aspergillus oryzae (mold) References: UniProt: E0SSW8, arabinogalactan endo-beta-1,4-galactanase #2: Chemical | #3: Chemical | ChemComp-HEZ / #4: Chemical | #5: 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: 1.99 Å3/Da / Density % sol: 38.06 % / Description: Needle |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 4% w/v 1,6 Hexanediol, 20 mM Magnesium chloride, 0,1 M HEPES pH 7.5 and 22 % w/v Polyacrylic acid 5100 sodium salt Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2014 / Details: KB mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→47.41 Å / Num. obs: 39320 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 26.25 Å2 / CC1/2: 0.97 / Rrim(I) all: 0.18 / Net I/σ(I): 5.58 |
Reflection shell | Resolution: 2.65→2.81 Å / Mean I/σ(I) obs: 1.43 / Num. unique obs: 5940 / CC1/2: 0.59 / Rrim(I) all: 0.787 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UR4 Resolution: 2.65→47.41 Å / SU ML: 0.3246 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.5664 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 23.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→47.41 Å
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Refine LS restraints |
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LS refinement shell |
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