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Yorodumi- PDB-8frd: Mouse acidic mammalian chitinase, catalytic domain in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8frd | |||||||||
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Title | Mouse acidic mammalian chitinase, catalytic domain in complex with N,N'-diacetylchitobiose at pH 5.25 | |||||||||
Components | Acidic mammalian chitinase | |||||||||
Keywords | HYDROLASE / GH18 chitinase / acidic mammalian chitinase | |||||||||
Function / homology | Function and homology information Digestion of dietary carbohydrate / production of molecular mediator involved in inflammatory response / chitinase / chitinase activity / chitin catabolic process / immune system process / chitin binding / polysaccharide catabolic process / positive regulation of chemokine production / kinase binding ...Digestion of dietary carbohydrate / production of molecular mediator involved in inflammatory response / chitinase / chitinase activity / chitin catabolic process / immune system process / chitin binding / polysaccharide catabolic process / positive regulation of chemokine production / kinase binding / apoptotic process / extracellular space / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | |||||||||
Authors | Diaz, R.E. / Fraser, J.S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biorxiv / Year: 2024 Title: Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. Authors: Diaz, R.E. / Ecker, A.K. / Correy, G.J. / Asthana, P. / Young, I.D. / Faust, B. / Thompson, M.C. / Seiple, I.B. / Van Dyken, S.J. / Locksley, R.M. / Fraser, J.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8frd.cif.gz | 379.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8frd.ent.gz | 252.1 KB | Display | PDB format |
PDBx/mmJSON format | 8frd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/8frd ftp://data.pdbj.org/pub/pdb/validation_reports/fr/8frd | HTTPS FTP |
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-Related structure data
Related structure data | 8fg5C 8fg7C 8fr9C 8fraC 8frbC 8frcC 8frgC 8gcaC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 44621.992 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Chia, Chia1 / Plasmid: mAMCase_CatD_6xHis_pTwistCMV / Cell line (production host): ExpiCHO-S / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q91XA9, chitinase #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: Chemical | #4: 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: 1.92 Å3/Da / Density % sol: 36.07 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.25 Details: 11 mg/mL AMCase catalytic domain 20% w/v PEG 6000 0.1 M Sodium Acetate pH 5.25 0.2 M Magnesium Chloride 29.00 mM GlcNAc2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11578 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11578 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→58.67 Å / Num. obs: 78163 / % possible obs: 98.72 % / Redundancy: 6.4 % / Biso Wilson estimate: 11.55 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1155 / Rpim(I) all: 0.04965 / Rrim(I) all: 0.126 / Net I/σ(I): 9.68 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 3.09 / Num. unique obs: 7593 / CC1/2: 0.68 / CC star: 0.9 / Rpim(I) all: 0.2425 / Rrim(I) all: 0.6197 / % possible all: 97.03 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→58.67 Å / SU ML: 0.1293 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 14.7232 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→58.67 Å
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Refine LS restraints |
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LS refinement shell |
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