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- PDB-1apz: HUMAN ASPARTYLGLUCOSAMINIDASE COMPLEX WITH REACTION PRODUCT -

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Basic information

Entry
Database: PDB / ID: 1apz
TitleHUMAN ASPARTYLGLUCOSAMINIDASE COMPLEX WITH REACTION PRODUCT
Components(ASPARTYLGLUCOSAMINIDASE) x 2
KeywordsCOMPLEX (HYDROLASE/PEPTIDE) / ASPARTYLGLUCOSAMINIDASE / GLYCOSYLASPARAGINASE / COMPLEX (HYDROLASE-PEPTIDE) / COMPLEX (HYDROLASE-PEPTIDE) complex
Function / homologyNeutrophil degranulation / Asparaginase / Nucleophile aminohydrolases, N-terminal / Peptidase T2, asparaginase 2 / N4-(beta-N-acetylglucosaminyl)-L-asparaginase / N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity / protein maturation / protein deglycosylation / protein self-association / azurophil granule lumen ...Neutrophil degranulation / Asparaginase / Nucleophile aminohydrolases, N-terminal / Peptidase T2, asparaginase 2 / N4-(beta-N-acetylglucosaminyl)-L-asparaginase / N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity / protein maturation / protein deglycosylation / protein self-association / azurophil granule lumen / peptidase activity / hydrolase activity / lysosome / neutrophil degranulation / endoplasmic reticulum / extracellular space / extracellular region / cytoplasm / N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / 2.3 Å resolution
AuthorsRouvinen, 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 14, 1995 / Release: Dec 23, 1996
RevisionDateData content typeGroupProviderType
1.0Dec 23, 1996Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASPARTYLGLUCOSAMINIDASE
B: ASPARTYLGLUCOSAMINIDASE
C: ASPARTYLGLUCOSAMINIDASE
D: ASPARTYLGLUCOSAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,30912
Polyers64,7574
Non-polymers1,5528
Water2,522140
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)17950
ΔGint (kcal/M)-90
Surface area (Å2)20690
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)98.400, 98.400, 134.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP 61

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide ASPARTYLGLUCOSAMINIDASE / / AGA / GLYCOSYLASPARAGINASE


Mass: 17293.336 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / Genus: Homo / Cell: LEUKOCYTEWhite blood cell
References: UniProt: P20933, N4-(beta-N-acetylglucosaminyl)-L-asparaginase
#2: Protein/peptide ASPARTYLGLUCOSAMINIDASE / / AGA / GLYCOSYLASPARAGINASE


Mass: 15085.118 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / Genus: Homo / Cell: LEUKOCYTEWhite blood cell
References: UniProt: P20933, N4-(beta-N-acetylglucosaminyl)-L-asparaginase

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Non-polymers , 4 types, 148 molecules

#3: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 5 / Details: COMPLEX WITH REACTION PRODUCT / Formula: C8H15NO6 / N-Acetylglucosamine
#4: Chemical ChemComp-ASP / ASPARTIC ACID


Mass: 133.103 Da / Num. of mol.: 2 / Formula: C4H7NO4 / Aspartic acid
#5: Chemical ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 / Density percent sol: 45 %
Crystal grow
*PLUS
Temp: 20 ℃ / pH: 4.9 / Method: vapor diffusion, hanging drop
Details: Tikkanen, R., (1996) Protein Struct. Func. Genet., 24, 253.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
110 mg/mlenzyme1drop
218 %(w/v)PEG40001reservoir
320 mMacetate1reservoir
41 mM1reservoirNaN3

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Data collection

SourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Collection date: Apr 10, 1994
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber obs: 26090 / Rmerge I obs: 0.0846 / Redundancy: 3 % / Percent possible obs: 75.4
Reflection
*PLUS
D resolution high: 2.3 Å / D resolution low: 15 Å / Number obs: 26051 / Number measured all: 79974 / Percent possible obs: 79.6
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.35 Å / Percent possible obs: 40.9

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Processing

Software
NameClassification
HKLdata collection
X-PLORrefinement
HKLdata reduction
RefineSigma F: 1
Displacement parametersB iso mean: 20.2 Å2
Least-squares processR factor R free: 0.291 / R factor R work: 0.212 / R factor obs: 0.212 / Highest resolution: 2.3 Å / Lowest resolution: 8 Å / Number reflection obs: 22717
Refine hist #LASTHighest resolution: 2.3 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 4520 / Nucleic acid: 0 / Ligand: 99 / Solvent: 140 / Total: 4759
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.010
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Least-squares process
*PLUS
R factor R free: 0.286 / R factor obs: 0.221
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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