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Yorodumi- PDB-4nfr: Human brain aspartoacylase mutant E285A complex with intermediate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nfr | ||||||
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Title | Human brain aspartoacylase mutant E285A complex with intermediate analog (N-phosphonomethyl-L-aspartate) | ||||||
Components | Aspartoacylase | ||||||
Keywords | HYDROLASE / Canavan disease / N-acetyl-L-aspartate / Zinc-dependent hydrolase / aspartoacylase family / aminoacylase-2 | ||||||
Function / homology | Function and homology information aspartoacylase / aspartoacylase activity / acetate metabolic process / aspartate metabolic process / central nervous system myelination / Aspartate and asparagine metabolism / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / positive regulation of oligodendrocyte differentiation / identical protein binding ...aspartoacylase / aspartoacylase activity / acetate metabolic process / aspartate metabolic process / central nervous system myelination / Aspartate and asparagine metabolism / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / positive regulation of oligodendrocyte differentiation / identical protein binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å | ||||||
Authors | Wijayasinghe, Y.S. / Pavlovsky, A.G. / Viola, R.E. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Aspartoacylase catalytic deficiency as the cause of canavan disease: a structural perspective. Authors: Wijayasinghe, Y.S. / Pavlovsky, A.G. / Viola, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nfr.cif.gz | 133 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nfr.ent.gz | 104.6 KB | Display | PDB format |
PDBx/mmJSON format | 4nfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nfr_validation.pdf.gz | 451.3 KB | Display | wwPDB validaton report |
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Full document | 4nfr_full_validation.pdf.gz | 456.2 KB | Display | |
Data in XML | 4nfr_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 4nfr_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/4nfr ftp://data.pdbj.org/pub/pdb/validation_reports/nf/4nfr | HTTPS FTP |
-Related structure data
Related structure data | 4mriC 4mxuC 4tnuC 2o4hS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 10 - 310 / Label seq-ID: 10 - 310
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-Components
#1: Protein | Mass: 35726.047 Da / Num. of mol.: 2 / Mutation: E285A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACY2, ASP, ASPA / Plasmid: PPICZA / Production host: Komagataella pastoris (fungus) / References: UniProt: P45381, aspartoacylase #2: Chemical | #3: Chemical | #4: 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: 3.92 Å3/Da / Density % sol: 68.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 14% PEG 3350, 0.05M sodium citrate, 0.3M potassium phosphate (dibasic), 3% ethylene glycol, 0.01M DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 29, 2013 / Details: Kirkpatrick-Baez mirrors |
Radiation | Monochromator: Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 17286 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 3 / Num. unique all: 377 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB Entry 2o4h Resolution: 3→46.76 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.89 / SU B: 16.388 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.445 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.212 Å2
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Refinement step | Cycle: LAST / Resolution: 3→46.76 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 18108 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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