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Yorodumi- PDB-6z2q: Crystal structure of wild type OgpA from Akkermansia muciniphila ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z2q | ||||||
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Title | Crystal structure of wild type OgpA from Akkermansia muciniphila in complex with an O-glycopeptide (GalGalNAc-TS) product | ||||||
Components |
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Keywords | HYDROLASE / O-glycan endopeptidase / mucins / OgpA. metalloprotease | ||||||
Function / homology | Function and homology information positive regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria / defense response to insect / response to bacterium / defense response / antibacterial humoral response / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Akkermansia muciniphila ATCC BAA-835 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.347 Å | ||||||
Authors | Trastoy, B. / Naegali, A. / Anso, I. / Sjogren, J. / Guerin, M.E. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila. Authors: Trastoy, B. / Naegeli, A. / Anso, I. / Sjogren, J. / Guerin, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z2q.cif.gz | 91 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z2q.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 6z2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/6z2q ftp://data.pdbj.org/pub/pdb/validation_reports/z2/6z2q | HTTPS FTP |
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-Related structure data
Related structure data | 6z2dSC 6z2oC 6z2pC 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
-Protein / Protein/peptide / Sugars , 3 types, 3 molecules AD
#1: Protein | Mass: 41856.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria) Gene: Amuc_1119 / Production host: Escherichia coli (E. coli) / References: UniProt: B2UR60 |
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#2: Protein/peptide | Mass: 2204.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P36193*PLUS |
#3: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen |
-Non-polymers , 4 types, 99 molecules
#4: Chemical | #5: Chemical | ChemComp-ACY / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.4 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 100mM sodium HEPES/MOPS pH 7.5, 100mM carboxylic acids mixture (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and sodium oxamate) ...Details: 100mM sodium HEPES/MOPS pH 7.5, 100mM carboxylic acids mixture (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and sodium oxamate) and 50% (w/v) of precipitant mix based on 40% (w/v) PEG 500 MME and 20% (w/v) PEG 20,000 (Morpheus protein crystallization screen). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 2.347→29.233 Å / Num. obs: 17627 / % possible obs: 98.62 % / Redundancy: 12.7 % / Biso Wilson estimate: 35.98 Å2 / CC1/2: 0.999 / CC star: 0.999 / Rmerge(I) obs: 0.1336 / Rrim(I) all: 0.1391 / Net I/σ(I): 19.29 |
Reflection shell | Resolution: 2.347→2.43 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.91 / Num. unique obs: 1530 / CC1/2: 0.2949 / CC star: 0.8 / Rrim(I) all: 1.007 / % possible all: 87.13 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Z2D Resolution: 2.347→29.233 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.21 / Stereochemistry target values: ML
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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 max: 74.02 Å2 / Biso mean: 37.1118 Å2 / Biso min: 25.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.347→29.233 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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