+Open data
-Basic information
Entry | Database: PDB / ID: 1apy | |||||||||
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Title | HUMAN ASPARTYLGLUCOSAMINIDASE | |||||||||
Components | (ASPARTYLGLUCOSAMINIDASE) x 2 | |||||||||
Keywords | HYDROLASE / ASPARTYLGLUCOSAMINIDASE / GLYCOSYLASPARAGINASE | |||||||||
Function / homology | Function and homology information N4-(beta-N-acetylglucosaminyl)-L-asparaginase / N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity / protein deglycosylation / azurophil granule lumen / peptidase activity / lysosome / Neutrophil degranulation / endoplasmic reticulum / proteolysis / extracellular space ...N4-(beta-N-acetylglucosaminyl)-L-asparaginase / N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity / protein deglycosylation / azurophil granule lumen / peptidase activity / lysosome / Neutrophil degranulation / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | |||||||||
Authors | Rouvinen, J. / Oinonen, C. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1995 Title: Three-dimensional structure of human lysosomal aspartylglucosaminidase. Authors: Oinonen, C. / Tikkanen, R. / Rouvinen, J. / Peltonen, L. #1: Journal: To be Published Title: Large-Scale Purification and Preliminary X-Ray Diffraction Studies of Human Aspartylglucosaminidase Authors: Tikkanen, R. / Rouvinen, J. / Torronen, A. / Kalkkinen, N. / Peltonen, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1apy.cif.gz | 126 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1apy.ent.gz | 102 KB | Display | PDB format |
PDBx/mmJSON format | 1apy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1apy_validation.pdf.gz | 489.6 KB | Display | wwPDB validaton report |
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Full document | 1apy_full_validation.pdf.gz | 493.6 KB | Display | |
Data in XML | 1apy_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 1apy_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/1apy ftp://data.pdbj.org/pub/pdb/validation_reports/ap/1apy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.8946, -0.055, 0.4435), Vector: |
-Components
#1: Protein | Mass: 17293.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: LEUKOCYTE References: UniProt: P20933, N4-(beta-N-acetylglucosaminyl)-L-asparaginase #2: Protein | Mass: 15085.118 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: LEUKOCYTE References: UniProt: P20933, N4-(beta-N-acetylglucosaminyl)-L-asparaginase #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 4.9 / Method: vapor diffusion, hanging dropDetails: Tikkanen, R., (1996) Protein Struct. Func. Genet., 24, 253. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 10, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 37933 / % possible obs: 72.9 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.0651 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 15 Å / Num. obs: 37768 / % possible obs: 76.2 % / Num. measured all: 95095 / Rmerge(I) obs: 0.0651 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.05 Å / % possible obs: 34.2 % |
-Processing
Software |
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Refinement | Resolution: 2→8 Å / σ(F): 1
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Displacement parameters | Biso mean: 30.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. reflection obs: 33326 / Rfactor obs: 0.169 / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.169 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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