+Open data
-Basic information
Entry | Database: PDB / ID: 8hmm | ||||||
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Title | Crystal structure of AoRhaA | ||||||
Components | Bac_rhamnosid6H domain-containing protein | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Alpha-L-rhamnosidase, six-hairpin glycosidase domain / Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / carbohydrate metabolic process / Alpha-L-rhamnosidase six-hairpin glycosidase domain-containing protein Function and homology information | ||||||
Biological species | Aspergillus oryzae RIB40 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Makabe, K. / Koseki, T. | ||||||
Funding support | 1items
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Citation | Journal: Proteins / Year: 2024 Title: Aspergillus oryzae alpha-l-rhamnosidase: Crystal structure and insight into the substrate specificity. Authors: Makabe, K. / Ishida, N. / Kanezaki, N. / Shiono, Y. / Koseki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hmm.cif.gz | 284.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hmm.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8hmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/8hmm ftp://data.pdbj.org/pub/pdb/validation_reports/hm/8hmm | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 69377.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Strain: RIB 40 / Gene: AO090003001291 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2UJB1 | ||||
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#2: Sugar | ChemComp-NAG / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.22 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 23% PEG3350 0.1M BisTris pH5.5 0.2M Ammonium Acetate 9 mg/mL protein |
-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: May 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→48.19 Å / Num. obs: 23315 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.16 Å2 / Rmerge(I) obs: 0.215 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.51→2.61 Å / Rmerge(I) obs: 0.829 / Num. unique obs: 2595 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.88 Å / SU ML: 0.2183 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.0985 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: 32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→19.88 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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