[English] 日本語
Yorodumi- PDB-4r4y: Structural basis of a point mutation that causes the genetic dise... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r4y | ||||||
---|---|---|---|---|---|---|---|
Title | Structural basis of a point mutation that causes the genetic disease Aspartylglucosaminuria | ||||||
Components | N(4)-(Beta-N-acetylglucosaminyl)-L-asparaginase | ||||||
Keywords | HYDROLASE / AGU structure / autoprocessing / glycosylasparaginase / lysosomal storage disease / pre-autoproteolysis trap | ||||||
Function / homology | Function and homology information N4-(beta-N-acetylglucosaminyl)-L-asparaginase / N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity / asparaginase activity / beta-aspartyl-peptidase activity / periplasmic space / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Elizabethkingia miricola (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sui, L. / Damodharan, L. / Pande, S. / Guo, H.C. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Structural Basis of a Point Mutation that Causes the Genetic Disease Aspartylglucosaminuria. Authors: Sui, L. / Lakshminarasimhan, D. / Pande, S. / Guo, H.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4r4y.cif.gz | 117.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4r4y.ent.gz | 91 KB | Display | PDB format |
PDBx/mmJSON format | 4r4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r4y_validation.pdf.gz | 449.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4r4y_full_validation.pdf.gz | 455.1 KB | Display | |
Data in XML | 4r4y_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 4r4y_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/4r4y ftp://data.pdbj.org/pub/pdb/validation_reports/r4/4r4y | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32237.668 Da / Num. of mol.: 2 / Fragment: UNP residues 46-340 / Mutation: G172D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia miricola (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: Q47898, N4-(beta-N-acetylglucosaminyl)-L-asparaginase #2: Chemical | ChemComp-SD4 / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.34 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 6.5 Details: 0.2M NaCl, 0.1M Bis-Tris pH 6.5, 25% PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI(111)CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 27448 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.052 / Rsym value: 0.06 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 9.5 / Rsym value: 0.113 / % possible all: 90.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.864 / SU B: 5.223 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 15.43 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→39 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|