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- PDB-1auk: HUMAN ARYLSULFATASE A -

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Basic information

Entry
Database: PDB / ID: 1auk
TitleHUMAN ARYLSULFATASE A
ComponentsARYLSULFATASE A
KeywordsHYDROLASE / CEREBROSIDE-3-SULFATE HYDROLYSIS / LYSOSOMAL ENZYME
Function / homologyC-terminal region of aryl-sulfatase / Sulfatase, N-terminal / Neutrophil degranulation / The activation of arylsulfatases / Glycosphingolipid metabolism / Sulfatases signature 1. / Sulfatases signature 2. / Sulfatase / Sulfatase, conserved site / Alkaline-phosphatase-like, core domain superfamily ...C-terminal region of aryl-sulfatase / Sulfatase, N-terminal / Neutrophil degranulation / The activation of arylsulfatases / Glycosphingolipid metabolism / Sulfatases signature 1. / Sulfatases signature 2. / Sulfatase / Sulfatase, conserved site / Alkaline-phosphatase-like, core domain superfamily / Alkaline phosphatase-like, alpha/beta/alpha / cerebroside-sulfatase / cerebroside-sulfatase activity / arylsulfatase activity / sulfuric ester hydrolase activity / glycosphingolipid metabolic process / lysosomal lumen / azurophil granule lumen / lysosome / endoplasmic reticulum lumen / neutrophil degranulation / calcium ion binding / extracellular exosome / extracellular region / Arylsulfatase A
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / 2.1 Å resolution
AuthorsLukatela, G. / Krauss, N. / Theis, K. / Gieselmann, V. / Von Figura, K. / Saenger, W.
CitationJournal: Biochemistry / Year: 1998
Title: Crystal structure of human arylsulfatase A: the aldehyde function and the metal ion at the active site suggest a novel mechanism for sulfate ester hydrolysis.
Authors: Lukatela, G. / Krauss, N. / Theis, K. / Selmer, T. / Gieselmann, V. / von Figura, K. / Saenger, W.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 29, 1997 / Release: Mar 4, 1998
RevisionDateData content typeGroupProviderType
1.0Mar 4, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance
1.3Jan 25, 2012Structure modelDerived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARYLSULFATASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4234
Polyers51,9571
Non-polymers4673
Water3,171176
1
A: ARYLSULFATASE A
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)419,38832
Polyers415,6548
Non-polymers3,73424
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area (Å2)22750
ΔGint (kcal/M)-114
Surface area (Å2)122670
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)132.630, 132.630, 192.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI 4 2 2

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Components

#1: Protein/peptide ARYLSULFATASE A / / CEREBROSIDE-3-SULFATE-SULFATASE


Mass: 51956.734 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Description: C-DNA EXPRESSION / Cellular location: LYSOSOME / Gene: ARSA / Organ: TESTISTesticle / Plasmid name: PBEH / Genus (production host): Mesocricetus
Cell line (production host): BABY HAMSTER KIDNEY CELLS (BHK)
Cellular location (production host): SECRETED ENZYME / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P15289, cerebroside-sulfatase
#2: Chemical ChemComp-NDG / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6
#3: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6 / N-Acetylglucosamine
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 / Density percent sol: 63 %
Crystal growTemp: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION IN HANGING DROPS AT 291 K. SOLUTION CONTAINING 10MG/ML PROTEIN, 10 MM TRIS/HCL (PH 7.4) AND 150 MM NACL WAS MIXED WITH SAME VOLUME OF RESERVOIR SOLUTION, CONTAINING 100 MM NA-ACETATE (PH 5.0 - 5.4) AND 10 - 13 % PEG 6000, vapor diffusion - hanging drop
PH range: 5.0-5.4
Crystal grow
*PLUS
Temp: 18 ℃ / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
1100 mMsodium acetate1reservoir
210-13 %PEG60001reservoir
3100 mMsodium acetate1drop
410-13 %PEG60001drop
51.25 %octyl-beta-glucopyranoside1drop
610 mMTris-HCl1drop
7150 mM1dropNaCl

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Data collection

DiffractionMean temperature: 277 kelvins
SourceSource: SYNCHROTRON / Type: SRS BEAMLINE PX9.5 / Synchrotron site: SRS / Beamline: PX9.5 / Wavelength: 0.91
DetectorType: MARRESEARCH / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Mar 1, 1996
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 34.97 Å2 / D resolution high: 2.1 Å / D resolution low: 3 Å / Number obs: 49794 / Observed criterion sigma I: -3 / Rsym value: 0.055 / NetI over sigmaI: 9.4 / Redundancy: 6.2 % / Percent possible obs: 96.1
Reflection shellHighest resolution: 2.1 Å / Lowest resolution: 2.2 Å / MeanI over sigI obs: 4.3 / Rsym value: 0.35 / Redundancy: 3.5 % / Percent possible all: 98
Reflection
*PLUS
Rmerge I obs: 0.063
Reflection shell
*PLUS
Percent possible obs: 96.7 / Rmerge I obs: 0.276

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
X-PLORphasing
RefineMethod to determine structure: MIRAS / R Free selection details: SHELLS / Sigma F: 0.5
Displacement parametersB iso mean: 43.1 Å2
Least-squares processR factor R free: 0.273 / R factor R work: 0.232 / R factor obs: 0.248 / Highest resolution: 2.1 Å / Lowest resolution: 3 Å / Number reflection R free: 2463 / Number reflection obs: 49794 / Percent reflection R free: 5 / Percent reflection obs: 98.6
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 3580 / Nucleic acid: 0 / Ligand: 29 / Solvent: 176 / Total: 3785
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d1.8
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Least-squares process
*PLUS
Number reflection all: 49794
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8

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