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- PDB-3h53: Crystal Structure of human alpha-N-acetylgalactosaminidase -

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Basic information

Entry
Database: PDB / ID: 3h53
TitleCrystal Structure of human alpha-N-acetylgalactosaminidase
ComponentsAlpha-N-acetylgalactosaminidase
KeywordsHYDROLASE / GLYCOPROTEIN / CARBOHYDRATE-BINDING PROTEIN / GLYCOSIDASE / LYSOSOMAL ENZYME / (BETA/ALPHA)8 BARREL / Disease mutation / Disulfide bond / Lysosome
Function / homology
Function and homology information


alpha-N-acetylgalactosaminidase / alpha-N-acetylgalactosaminidase activity / glycolipid catabolic process / alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / carbohydrate catabolic process / lysosome / protein homodimerization activity / extracellular exosome / cytoplasm
Similarity search - Function
Alpha galactosidase A, C-terminal beta-sandwich domain / Alpha galactosidase A C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel ...Alpha galactosidase A, C-terminal beta-sandwich domain / Alpha galactosidase A C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Alpha-N-acetylgalactosaminidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsClark, N.E. / Garman, S.C.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The 1.9 a structure of human alpha-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases
Authors: Clark, N.E. / Garman, S.C.
History
DepositionApr 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
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_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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
Revision 2.1Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-N-acetylgalactosaminidase
B: Alpha-N-acetylgalactosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,29925
Polymers91,1662
Non-polymers5,13323
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint46 kcal/mol
Surface area30720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.532, 114.260, 68.408
Angle α, β, γ (deg.)90.000, 96.110, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEUAA18 - 3101 - 293
21LEULEULEULEUBB18 - 3101 - 293
12GLYGLYLYSLYSAA311 - 404294 - 387
22GLYGLYLYSLYSBB311 - 404294 - 387

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-N-acetylgalactosaminidase / Alpha-galactosidase B


Mass: 45582.867 Da / Num. of mol.: 2 / Mutation: N201Q
Source method: isolated from a genetically manipulated source
Details: Selected with blastocidin / Source: (gene. exp.) Homo sapiens (human) / Gene: NAGA / Plasmid: pIB/V5-His-TOPO TA / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): HI-FIVE
References: UniProt: P17050, alpha-N-acetylgalactosaminidase

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Sugars , 4 types, 6 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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.: 2
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 , 2 types, 752 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 3.27 Å3/Da / Density % sol: 62.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: PEG3350, citric acid, Bis-Tris propane, pH 4.1, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 12, 2008 / Details: Osmic Blue
RadiationMonochromator: Osmic Blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 77785 / % possible obs: 99.3 % / Redundancy: 9.9 % / Biso Wilson estimate: 39.9 Å2 / Rsym value: 0.085 / Net I/σ(I): 29
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 7283 / Rsym value: 0.61 / % possible all: 93

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.5.0070refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KTB

1ktb


Resolution: 2.01→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.73 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.194 3916 5 %RANDOM
Rwork0.161 ---
obs0.163 77775 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.76 Å2 / Biso mean: 29.358 Å2 / Biso min: 14.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å23.62 Å2
2---1.85 Å20 Å2
3---1.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.124 Å0.133 Å
Refinement stepCycle: LAST / Resolution: 2.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6162 0 339 735 7236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226714
X-RAY DIFFRACTIONr_angle_refined_deg1.0482.0059137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5985778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70624.086301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.364151041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1361540
X-RAY DIFFRACTIONr_chiral_restr0.0720.21002
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214980
X-RAY DIFFRACTIONr_mcbond_it2.07983876
X-RAY DIFFRACTIONr_mcangle_it2.952126251
X-RAY DIFFRACTIONr_scbond_it2.94782838
X-RAY DIFFRACTIONr_scangle_it4.299122886
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2305MEDIUM POSITIONAL0.170.5
1A2305MEDIUM THERMAL2.1310
2B746MEDIUM POSITIONAL0.240.5
2B746MEDIUM THERMAL2.2110
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 290 -
Rwork0.259 5069 -
all-5359 -
obs--93.44 %
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)
10.94690.1692-0.24150.5494-0.14310.37160.0497-0.00380.10920.02510.025-0.0338-0.03850.0351-0.07480.0377-0.00330.01850.0152-0.01090.032256.4433-1.14429.9794
21.1474-0.1637-0.05280.9985-0.31380.40470.06990.10820.21390.05930.12980.3061-0.1077-0.1483-0.19970.04730.0380.06030.06430.09520.177225.77233.388610.8318
31.03880.3481-0.45731.053-0.43170.5144-0.0720.0858-0.03570.05160.16120.2710.0448-0.0846-0.08920.0455-0.00530.01630.03720.04690.09621.7222-31.596721.6606
41.25260.3092-0.38591.1062-0.26830.6482-0.1074-0.0439-0.3085-0.0265-0.0297-0.26030.1650.13510.13710.05660.03680.02850.03190.02160.12351.1721-37.13216.1906
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 310
2X-RAY DIFFRACTION2A311 - 404
3X-RAY DIFFRACTION3B18 - 310
4X-RAY DIFFRACTION4B311 - 404

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