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Yorodumi- PDB-2o4h: Human brain aspartoacylase complex with intermediate analog (N-ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o4h | ||||||
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Title | Human brain aspartoacylase 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 / ACY2 / ASPA / N-phosphonomethyl-L-aspartate | ||||||
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: 2.7 Å | ||||||
Authors | Le Coq, J. / Pavlovsky, A. / Sanishvili, R. / Viola, R.E. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Examination of the Mechanism of Human Brain Aspartoacylase through the Binding of an Intermediate Analogue. Authors: Le Coq, J. / Pavlovsky, A. / Malik, R. / Sanishvili, R. / Xu, C. / 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 | 2o4h.cif.gz | 133.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o4h.ent.gz | 104.4 KB | Display | PDB format |
PDBx/mmJSON format | 2o4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o4h_validation.pdf.gz | 458.5 KB | Display | wwPDB validaton report |
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Full document | 2o4h_full_validation.pdf.gz | 467.8 KB | Display | |
Data in XML | 2o4h_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 2o4h_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/2o4h ftp://data.pdbj.org/pub/pdb/validation_reports/o4/2o4h | HTTPS FTP |
-Related structure data
Related structure data | 2o53C 2i3cS 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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Details | The second part of the biological assembly is generated by the two fold axis: -x, -y, z. |
-Components
#1: Protein | Mass: 35784.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASPA, ACY2, ASP / Organ: Brain / Plasmid: pPICZA / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / 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: 3.74 Å3/Da / Density % sol: 67.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 8-10 mg/ml Protein, 50 mM Sodium citrate pH 6.0, 300 mM K2HPO4, 15-19% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.283 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2006 / Details: Kirkpatrick-Baez pair of focusing bimorph mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.283 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 28991 / Num. obs: 27490 / % possible obs: 95.3 % / Redundancy: 10.7 % / Biso Wilson estimate: 72.7 Å2 / Rsym value: 0.094 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1849 / Rsym value: 0.354 / % possible all: 62.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2I3C Resolution: 2.7→46.47 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.892 / SU B: 25.812 / SU ML: 0.25 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.451 / ESU R Free: 0.321 / 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: 59.981 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→46.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -43.762 Å / Origin y: 15.699 Å / Origin z: -30.254 Å
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Refinement TLS group |
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