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- PDB-4fdi: The molecular basis of mucopolysaccharidosis IV A -

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Basic information

Entry
Database: PDB / ID: 4fdi
TitleThe molecular basis of mucopolysaccharidosis IV A
ComponentsN-acetylgalactosamine-6-sulfatase
KeywordsHYDROLASE / glycoprotein / enzyme replacement therapy / sulfatase / formylglycine / N-linked glycosylation / lysosomal enzyme
Function / homology
Function and homology information


N-acetylgalactosamine-6-sulfatase / N-acetylgalactosamine-6-sulfatase activity / MPS IV - Morquio syndrome A / N-acetylgalactosamine-4-sulfatase activity / Keratan sulfate degradation / arylsulfatase activity / sulfuric ester hydrolase activity / lysosomal lumen / azurophil granule lumen / Neutrophil degranulation ...N-acetylgalactosamine-6-sulfatase / N-acetylgalactosamine-6-sulfatase activity / MPS IV - Morquio syndrome A / N-acetylgalactosamine-4-sulfatase activity / Keratan sulfate degradation / arylsulfatase activity / sulfuric ester hydrolase activity / lysosomal lumen / azurophil granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / metal ion binding
Similarity search - Function
N-acetylgalactosamine-6-sulfatase / C-terminal region of aryl-sulfatase / Arylsulfatase, C-terminal domain - #10 / : / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Arylsulfatase, C-terminal domain / Sulfatase, N-terminal / Sulfatase ...N-acetylgalactosamine-6-sulfatase / C-terminal region of aryl-sulfatase / 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
CITRIC ACID / N-acetylgalactosamine-6-sulfatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsRivera-Colon, Y. / Garman, S.C.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The Structure of Human GALNS Reveals the Molecular Basis for Mucopolysaccharidosis IV A.
Authors: Rivera-Colon, Y. / Schutsky, E.K. / Kita, A.Z. / Garman, S.C.
History
DepositionMay 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_nonpoly.name / _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.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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Dec 6, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylgalactosamine-6-sulfatase
B: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,13612
Polymers112,6032
Non-polymers1,53310
Water13,962775
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.372, 155.522, 62.555
Angle α, β, γ (deg.)90.000, 113.760, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 4 / Auth seq-ID: 30 - 520 / Label seq-ID: 4 - 494

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein N-acetylgalactosamine-6-sulfatase / GALNS / Chondroitinsulfatase / Chondroitinase / Galactose-6-sulfate sulfatase / N- ...GALNS / Chondroitinsulfatase / Chondroitinase / Galactose-6-sulfate sulfatase / N-acetylgalactosamine-6-sulfate sulfatase / GalNAc6S sulfatase


Mass: 56301.426 Da / Num. of mol.: 2 / Fragment: UNP residues 27-522
Source method: isolated from a genetically manipulated source
Details: Selected with blastocidin / Source: (gene. exp.) Homo sapiens (human) / Gene: GALNS / Plasmid: pIB/V5-His-TOPO TA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): HI-FIVE
References: UniProt: P34059, N-acetylgalactosamine-6-sulfatase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 781 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10-15% PEG6000, 0.1 M citric acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2010 / Details: focusing mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 54154 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.38 Å2 / Rsym value: 0.11 / Χ2: 1.049 / Net I/σ(I): 14.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.277 / Num. unique all: 2676 / Χ2: 0.971 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N2K

1n2k


Resolution: 2.2→45.53 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.648 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.265 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2749 5.1 %RANDOM
Rwork0.1637 ---
obs0.1661 54075 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.09 Å2 / Biso mean: 22.8931 Å2 / Biso min: 5.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.06 Å2
2---0.71 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7796 0 96 775 8667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228164
X-RAY DIFFRACTIONr_angle_refined_deg1.11.9611145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6465992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47423.708383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.628151226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8281548
X-RAY DIFFRACTIONr_chiral_restr0.0710.21171
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216424
X-RAY DIFFRACTIONr_mcbond_it1.62764934
X-RAY DIFFRACTIONr_mcangle_it2.44387951
X-RAY DIFFRACTIONr_scbond_it3.63293230
X-RAY DIFFRACTIONr_scangle_it5.343183190
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3866 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.1610
MEDIUM THERMAL0.52
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 210 -
Rwork0.183 3757 -
all-3967 -
obs--99.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.66140.09030.01391.92790.27520.24020.0018-0.0433-0.02050.2318-0.02340.15020.0338-0.0150.02160.0489-0.01060.02120.0276-0.00640.01454.16-0.13415.353
20.4808-0.0597-0.20092.76590.38940.6188-0.0460.1295-0.035-0.46430.1279-0.5095-0.09980.1085-0.08190.0989-0.05220.08060.085-0.04660.121922.9074.234-2.553
33.59270.5306-0.02611.25190.95651.1931-0.04510.2657-0.1202-0.1623-0.06660.3421-0.0551-0.08150.11170.0829-0.0185-0.06230.0629-0.03610.2163-7.363-12.618-2.013
40.61530.1489-0.01741.6721-0.24710.24680.0082-0.04850.00360.2075-0.0329-0.1956-0.02740.00680.02460.0408-0.0078-0.04720.02410.00960.057726.42338.20416.037
50.66570.1250.08642.2408-0.56560.4895-0.10430.16750.1086-0.42210.14660.4250.0899-0.0683-0.04240.0901-0.0458-0.08880.06550.0370.10837.48334.756-2.163
61.37950.4127-0.33171.3343-0.72730.9285-0.03580.07340.0904-0.1924-0.0508-0.38460.03720.0770.08650.0685-0.01630.02020.04180.04120.255338.65251.623-0.475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 379
2X-RAY DIFFRACTION2A380 - 480
3X-RAY DIFFRACTION3A481 - 522
4X-RAY DIFFRACTION4B29 - 379
5X-RAY DIFFRACTION5B380 - 480
6X-RAY DIFFRACTION6B481 - 520

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