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- PDB-1fsu: Crystal Structure of 4-Sulfatase (human) -

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Basic information

Entry
Database: PDB / ID: 1fsu
TitleCrystal Structure of 4-Sulfatase (human)
ComponentsN-ACETYLGALACTOSAMINE-4-SULFATASE
KeywordsHYDROLASE / SULFATASE / GLYCOSAMINOGLYCAN DEGRADATION / GLYCOPROTEIN / LYSOSOME
Function / homology
Function and homology information


N-acetylgalactosamine-4-sulfatase / colon epithelial cell migration / MPS VI - Maroteaux-Lamy syndrome / N-acetylgalactosamine-4-sulfatase activity / Glycosphingolipid metabolism / chondroitin sulfate catabolic process / The activation of arylsulfatases / CS/DS degradation / arylsulfatase activity / neutrophil degranulation ...N-acetylgalactosamine-4-sulfatase / colon epithelial cell migration / MPS VI - Maroteaux-Lamy syndrome / N-acetylgalactosamine-4-sulfatase activity / Glycosphingolipid metabolism / chondroitin sulfate catabolic process / The activation of arylsulfatases / CS/DS degradation / arylsulfatase activity / neutrophil degranulation / regulation of epithelial cell migration / response to methylmercury / response to pH / lysosomal transport / lysosome organization / rough endoplasmic reticulum / lysosomal lumen / response to nutrient / central nervous system development / positive regulation of neuron projection development / autophagy / response to estrogen / azurophil granule lumen / ficolin-1-rich granule lumen / lysosome / endoplasmic reticulum lumen / Neutrophil degranulation / Golgi apparatus / cell surface / mitochondrion / extracellular exosome / extracellular region / metal ion binding
Similarity search - Function
Arylsulfatase, C-terminal domain - #10 / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Arylsulfatase, C-terminal domain / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily ...Arylsulfatase, C-terminal domain - #10 / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Arylsulfatase, C-terminal domain / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsBond, C. / Guss, M.
CitationJournal: Structure / Year: 1997
Title: Structure of a human lysosomal sulfatase.
Authors: Bond, C.S. / Clements, P.R. / Ashby, S.J. / Collyer, C.A. / Harrop, S.J. / Hopwood, J.J. / Guss, J.M.
History
DepositionJul 29, 1996Processing site: BNL
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 2, 2015Group: Non-polymer description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ACETYLGALACTOSAMINE-4-SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7435
Polymers55,8191
Non-polymers9244
Water4,864270
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.000, 107.000, 144.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein N-ACETYLGALACTOSAMINE-4-SULFATASE / / ARYLSULFATASE B / ASB / 4-SULFATASE


Mass: 55819.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: LYSOSOME / Gene: G4S / Organ: LIVER / Cell line (production host): CHO452 / Cellular location (production host): SECRETED / Organelle (production host): LYSOSOME / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): K1
References: UniProt: P15848, N-acetylgalactosamine-4-sulfatase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

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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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.1
Details: HANGING DROPS, 0.2 M MALATE/ 0.1 M ACETATE BUFFERED AT PH 5.1. 12-15 % PEG8000, 20% GLYCEROL., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Ashby, S.J., (1995) Acta Cryst. D, 51, 1082.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.025 Mpotassium phosphate1drop
310 %PEG80001drop
40.2 Mpotassium phosphate1reservoir
514 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 27332 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 7.9 Å2 / Rsym value: 0.089
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.9 % / Rsym value: 0.25 / % possible all: 72.9
Reflection
*PLUS
Num. measured all: 194673 / Rmerge(I) obs: 0.089

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Highest resolution: 2.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1032 3.7 %RANDOM
Rwork0.188 ---
obs0.188 27332 92 %-
Displacement parametersBiso mean: 23.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-6 Å
Luzzati sigma a-0.27 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3811 0 58 270 4139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.08
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.258 83 3.9 %
Rwork0.243 2047 -
obs--73 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 9999 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.08

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