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- PDB-4fdj: The molecular basis of mucopolysaccharidosis IV A, complex with GalNAc -

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Basic information

Entry
Database: PDB / ID: 4fdj
TitleThe molecular basis of mucopolysaccharidosis IV A, complex with GalNAc
ComponentsN-acetylgalactosamine-6-sulfatase
KeywordsHYDROLASE / glycoprotein / enzyme replacement therapy / sulfatase / carbohydrate-binding protein / 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 / Alkaline Phosphatase, subunit A ...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
2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetylgalactosamine-6-sulfatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.81 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 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

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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)114,01010
Polymers112,6032
Non-polymers1,4078
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.706, 155.835, 61.801
Angle α, β, γ (deg.)90.000, 113.430, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A30 - 375
2111B30 - 375
1211A376 - 380
2211B376 - 380
1311A381 - 466
2311B381 - 466
1412A467 - 471
2412B467 - 471
1511A472 - 520
2511B472 - 520
1611A604 - 1001
2611B604 - 1001

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Components

#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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
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: NSLS / Beamline: X6A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 23, 2011 / Details: toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 24690 / % possible obs: 96.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 39.07 Å2 / Rsym value: 0.143 / Χ2: 1.202 / Net I/σ(I): 8.6
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.278 / Num. unique all: 1055 / Χ2: 0.806 / % possible all: 83.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4FDI

4fdi


Resolution: 2.81→45.31 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.868 / Occupancy max: 1 / Occupancy min: 1 / SU B: 39.286 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 1269 5.1 %FROM PDB ENTRY 4FDI
Rwork0.2066 ---
obs0.2089 24664 95.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 110.7 Å2 / Biso mean: 39.9954 Å2 / Biso min: 10.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0.21 Å2
2---0.19 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.81→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7787 0 88 205 8080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228132
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.96111097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5235983
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06823.717382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7341548
X-RAY DIFFRACTIONr_chiral_restr0.0730.21171
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0226382
X-RAY DIFFRACTIONr_mcbond_it1.43964922
X-RAY DIFFRACTIONr_mcangle_it2.48387926
X-RAY DIFFRACTIONr_scbond_it3.50893210
X-RAY DIFFRACTIONr_scangle_it5.58183171
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
3878TIGHT POSITIONAL0.020.05
19MEDIUM POSITIONAL0.020.5
3878TIGHT THERMAL0.050.5
19MEDIUM THERMAL0.032
LS refinement shellResolution: 2.81→2.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 71 -
Rwork0.31 1377 -
all-1448 -
obs--76.82 %
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)
11.61380.22720.06452.0860.11890.6478-0.0247-0.1368-0.140.18940.01270.41320.1072-0.01440.0120.13150.0120.03960.19120.0060.12283.959-0.16215.403
22.2396-0.3305-1.07523.37980.05630.7254-0.010.2542-0.0446-0.54990.0288-0.47540.1481-0.1083-0.01880.2492-0.06640.01920.2611-0.05620.129422.7734.089-2.618
38.2169-0.40870.93230.4772-0.60161.68140.34760.9874-0.0315-0.0287-0.00440.46740.1595-0.263-0.34320.2971-0.0499-0.02020.2461-0.0280.5751-8.048-13.145-1.607
41.71150.3559-0.01921.8734-0.38620.4534-0.003-0.1320.14380.2264-0.0514-0.3758-0.03480.01050.05440.17420.0017-0.05580.2099-0.0190.115426.18138.06816.259
52.59980.15480.6093.9454-1.21291.9028-0.02550.27480.1094-0.67030.06850.8254-0.10780.0514-0.0430.2297-0.054-0.15140.20320.02930.2367.42534.573-2.109
65.1564-1.57280.47452.1963-2.30942.8293-0.09080.80680.3056-0.1348-0.3095-0.45020.16680.26150.40040.2449-0.0581-0.05840.2547-0.0010.637738.28551.554-0.213
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 379
2X-RAY DIFFRACTION2A380 - 480
3X-RAY DIFFRACTION3A481 - 520
4X-RAY DIFFRACTION4B29 - 379
5X-RAY DIFFRACTION5B380 - 480
6X-RAY DIFFRACTION6B481 - 520

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