+Open data
-Basic information
Entry | Database: PDB / ID: 3fxy | ||||||
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Title | Acidic Mammalian Chinase, Catalytic Domain | ||||||
Components | Acidic mammalian chitinase | ||||||
Keywords | HYDROLASE / CHITINASE / ASTHMA / CHITIN DEGRADATION / Alternative splicing / Carbohydrate metabolism / Chitin-binding / Cytoplasm / Glycosidase / Polymorphism / Polysaccharide degradation / Secreted | ||||||
Function / homology | Function and homology information chitin metabolic process / production of molecular mediator involved in inflammatory response / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / immune system process / chitin binding / polysaccharide catabolic process ...chitin metabolic process / production of molecular mediator involved in inflammatory response / polysaccharide digestion / Digestion of dietary carbohydrate / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Olland, A.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Triad of polar residues implicated in pH specificity of acidic mammalian chitinase. Authors: Olland, A.M. / Strand, J. / Presman, E. / Czerwinski, R. / Joseph-McCarthy, D. / Krykbaev, R. / Schlingmann, G. / Chopra, R. / Lin, L. / Fleming, M. / Kriz, R. / Stahl, M. / Somers, W. / Fitz, L. / Mosyak, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fxy.cif.gz | 298.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fxy.ent.gz | 251.4 KB | Display | PDB format |
PDBx/mmJSON format | 3fxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/3fxy ftp://data.pdbj.org/pub/pdb/validation_reports/fx/3fxy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 44203.371 Da / Num. of mol.: 4 / Fragment: UNP residues 22-408 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHIA / Production host: Chinese Hamster (Chinese hamster) / References: UniProt: Q9BZP6, chitinase #2: Water | ChemComp-HOH / | Sequence details | ACCORDING TO THE AUTHORS THESE POSITIONS ARE LABELED AS SNPS. THIS WAS THE SEQUENCE THE AUTHORS GOT ...ACCORDING TO THE AUTHORS THESE POSITIONS ARE LABELED AS SNPS. THIS WAS THE SEQUENCE THE AUTHORS GOT IN ALL CLONES WHEN THEY CLONED AMCASE, AND SINCE SNP FREQUENCY WAS NOT INDICATED IN THE GENOMIC DATABASE, THEY KEPT THIS CLONE. | |
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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: 2.03 Å3/Da / Density % sol: 39.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 15% PEG 3350, 120 mM ammonium sulfate, 60 mM sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 1, 2004 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 93507 / Num. obs: 91479 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 9.77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.15 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.228 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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