+Open data
-Basic information
Entry | Database: PDB / ID: 7ebq | ||||||||||||
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Title | The structural analysis of A.Muciniphila sulfatase | ||||||||||||
Components | Sulfatase | ||||||||||||
Keywords | HYDROLASE / Akkermansia Muciniphila Sulfatase Mucin | ||||||||||||
Function / homology | N-sulphoglucosamine sulphohydrolase, C-terminal / N-sulphoglucosamine sulphohydrolase, C-terminal / Sulfatases signature 1. / Sulfatase, conserved site / sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / Sulfatase Function and homology information | ||||||||||||
Biological species | Akkermansia muciniphila (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||||||||
Authors | Bao, R. / Li, C.C. / Tang, X.Y. / Zhu, Y.B. / Song, Y.J. / Zhao, N.L. / Huang, Q. / Mou, X.Y. / Luo, G.H. / Liu, T.G. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Structural analysis of the sulfatase AmAS from Akkermansia muciniphila. Authors: Li, C.C. / Tang, X.Y. / Zhu, Y.B. / Song, Y.J. / Zhao, N.L. / Huang, Q. / Mou, X.Y. / Luo, G.H. / Liu, T.G. / Tong, A.P. / Tang, H. / Bao, R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ebq.cif.gz | 254.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ebq.ent.gz | 178.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ebq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ebq_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7ebq_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7ebq_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 7ebq_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/7ebq ftp://data.pdbj.org/pub/pdb/validation_reports/eb/7ebq | HTTPS FTP |
-Related structure data
Related structure data | 7ebpC 5g2vS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 60727.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Akkermansia muciniphila (strain ATCC BAA-835 / Muc) (bacteria) Strain: ATCC BAA-835 / Muc / Gene: Amuc_1074 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2UR15 |
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#2: Sugar | ChemComp-NAG / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.1 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.08M Sodium HEPES, 23% w/v PEG 8000, pH7.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.44 Å / Num. obs: 30831 / % possible obs: 99.7 % / Redundancy: 8.5 % / Biso Wilson estimate: 30.87 Å2 / Rrim(I) all: 0.222 / Net I/σ(I): 5.16 |
Reflection shell | Resolution: 2.3→2.37 Å / Num. unique obs: 3030 / Rrim(I) all: 0.834 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5g2v Resolution: 2.4→39.44 Å / SU ML: 0.3461 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.9733 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: 38.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→39.44 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -7.19377293185 Å / Origin y: -3.96787747983 Å / Origin z: 19.6641498323 Å
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Refinement TLS group | Selection details: all |