+Open data
-Basic information
Entry | Database: PDB / ID: 7mhu | ||||||
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Title | Sialidase24 apo | ||||||
Components | Exo-alpha-sialidase | ||||||
Keywords | HYDROLASE / Sialidase / microbiome / sialic acid / inflammation | ||||||
Function / homology | BNR repeat-like domain / exo-alpha-sialidase activity / Sialidase family / Sialidase / Sialidase superfamily / Exo-alpha-sialidase Function and homology information | ||||||
Biological species | Bacteroides acidifaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Rees, S.D. / Chang, G.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proteins / Year: 2021 Title: Computational models in the service of X-ray and cryo-electron microscopy structure determination. Authors: Kryshtafovych, A. / Moult, J. / Albrecht, R. / Chang, G.A. / Chao, K. / Fraser, A. / Greenfield, J. / Hartmann, M.D. / Herzberg, O. / Josts, I. / Leiman, P.G. / Linden, S.B. / Lupas, A.N. / ...Authors: Kryshtafovych, A. / Moult, J. / Albrecht, R. / Chang, G.A. / Chao, K. / Fraser, A. / Greenfield, J. / Hartmann, M.D. / Herzberg, O. / Josts, I. / Leiman, P.G. / Linden, S.B. / Lupas, A.N. / Nelson, D.C. / Rees, S.D. / Shang, X. / Sokolova, M.L. / Tidow, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mhu.cif.gz | 154.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mhu.ent.gz | 121.2 KB | Display | PDB format |
PDBx/mmJSON format | 7mhu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mhu_validation.pdf.gz | 432.3 KB | Display | wwPDB validaton report |
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Full document | 7mhu_full_validation.pdf.gz | 435.9 KB | Display | |
Data in XML | 7mhu_validation.xml.gz | 27 KB | Display | |
Data in CIF | 7mhu_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/7mhu ftp://data.pdbj.org/pub/pdb/validation_reports/mh/7mhu | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 45777.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides acidifaciens (bacteria) / Gene: E5356_01515 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A4S2B3K9 #2: 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: 2.96 Å3/Da / Density % sol: 58.51 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Bis-Tris, 20% polyethylene glycol monomethyl ether 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.62 Å / Num. obs: 73015 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.272 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2→2.04 Å / Num. unique obs: 4481 / CC1/2: 0.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold T1089TS427_2 Resolution: 2→29.62 Å / Cross valid method: FREE R-VALUE / σ(F): 143.18 / Phase error: 40.02 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.62 Å
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Refine LS restraints |
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LS refinement shell |
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