+Open data
-Basic information
Entry | Database: PDB / ID: 1apz | |||||||||
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Title | HUMAN ASPARTYLGLUCOSAMINIDASE COMPLEX WITH REACTION PRODUCT | |||||||||
Components | (ASPARTYLGLUCOSAMINIDASE) x 2 | |||||||||
Keywords | COMPLEX (HYDROLASE/PEPTIDE) / ASPARTYLGLUCOSAMINIDASE / GLYCOSYLASPARAGINASE / COMPLEX (HYDROLASE-PEPTIDE) / COMPLEX (HYDROLASE-PEPTIDE) complex | |||||||||
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: 2.3 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 | 1apz.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1apz.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 1apz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1apz_validation.pdf.gz | 507.7 KB | Display | wwPDB validaton report |
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Full document | 1apz_full_validation.pdf.gz | 518.9 KB | Display | |
Data in XML | 1apz_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 1apz_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/1apz ftp://data.pdbj.org/pub/pdb/validation_reports/ap/1apz | 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: (-0.8936, -0.0543, 0.4456), Vector: |
-Components
-Protein , 2 types, 4 molecules ACBD
#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 |
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-Sugars , 2 types, 4 molecules
#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 Details: COMPLEX WITH REACTION PRODUCT |
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#4: Sugar |
-Non-polymers , 2 types, 142 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||
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 RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 10, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 26090 / % possible obs: 75.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.0846 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 15 Å / Num. obs: 26051 / % possible obs: 79.6 % / Num. measured all: 79974 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.35 Å / % possible obs: 40.9 % |
-Processing
Software |
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Refinement | Resolution: 2.3→8 Å / σ(F): 1
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Displacement parameters | Biso mean: 20.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.221 / Rfactor Rfree: 0.286 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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