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- PDB-3hg4: Human alpha-galactosidase catalytic mechanism 3. Covalent intermediate -

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Basic information

Entry
Database: PDB / ID: 3hg4
TitleHuman alpha-galactosidase catalytic mechanism 3. Covalent intermediate
ComponentsAlpha-galactosidase A
KeywordsHYDROLASE / GLYCOPROTEIN / CARBOHYDRATE-BINDING PROTEIN / GLYCOSIDASE / LYSOSOMAL ENZYME / (BETA/ALPHA)8 BARREL / Disease mutation / Disulfide bond / Lysosome
Function / homology
Function and homology information


glycosylceramide catabolic process / negative regulation of nitric-oxide synthase activity / alpha-galactosidase / glycosphingolipid catabolic process / galactoside binding / alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / negative regulation of nitric oxide biosynthetic process / Glycosphingolipid catabolism ...glycosylceramide catabolic process / negative regulation of nitric-oxide synthase activity / alpha-galactosidase / glycosphingolipid catabolic process / galactoside binding / alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / negative regulation of nitric oxide biosynthetic process / Glycosphingolipid catabolism / catalytic activity / lysosomal lumen / azurophil granule lumen / lysosome / hydrolase activity / signaling receptor binding / Neutrophil degranulation / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / 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
2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose / ACETIC ACID / beta-D-galactopyranose / Alpha-galactosidase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsGuce, A.I. / Clark, N.E. / Garman, S.C.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Catalytic mechanism of human alpha-galactosidase.
Authors: Guce, A.I. / Clark, N.E. / Salgado, E.N. / Ivanen, D.R. / Kulminskaya, A.A. / Brumer, H. / Garman, S.C.
History
DepositionMay 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / struct_asym / struct_conn / 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_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: 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 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-galactosidase A
B: Alpha-galactosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,50618
Polymers90,7892
Non-polymers4,71716
Water12,286682
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint19 kcal/mol
Surface area31280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.218, 90.218, 216.615
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLYGLYAA32 - 3281 - 297
21LEULEUGLYGLYBB32 - 3281 - 297
12TYRTYRMETMETAA329 - 421298 - 390
22TYRTYRMETMETBB329 - 421298 - 390

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-galactosidase A / Alpha-D-galactoside galactohydrolase / Alpha-D-galactosidase A / Melibiase


Mass: 45394.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLA / Production host: Homo sapiens (human) / References: UniProt: P06280, alpha-galactosidase

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Sugars , 6 types, 9 molecules

#2: 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.: 2
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
#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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
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
#5: Sugar ChemComp-7JZ / 2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose / 2-DEOXY-2,2-DIFLUORO-BETA-D-GALACTOPYRANOSYL-ENZYME INTERMEDIATE / 2-deoxy-2,2-difluoro-beta-D-lyxo-hexose / 2-deoxy-2,2-difluoro-D-lyxo-hexose / 2-deoxy-2,2-difluoro-lyxo-hexose


Type: D-saccharide, beta linking / Mass: 200.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10F2O5
#8: 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.: 1
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
#9: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 689 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4000, Ammonium Sulfate, Sodium Acetate, pH 4.6, 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 / 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
ReflectionRedundancy: 15.9 % / Av σ(I) over netI: 28.33 / Number: 739029 / Rmerge(I) obs: 0.112 / Χ2: 1.01 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 46337 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.955097.510.0361.07915.2
3.934.9599.910.0471.19815.9
3.443.9310010.0831.0315.8
3.123.4410010.1351.02316.1
2.93.1210010.2251.02316.2
2.732.910010.3250.96816.2
2.592.7310010.4530.99815.9
2.482.5910010.6040.9416.1
2.382.4810010.7690.93716.1
2.32.3810010.9440.90616
ReflectionResolution: 2.3→50 Å / Num. obs: 46337 / % possible obs: 99.7 % / Redundancy: 15.9 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Χ2: 1.01 / Net I/σ(I): 28.328
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 16 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4548 / Rsym value: 0.944 / Χ2: 0.906 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: human alpha-galactosidase

Resolution: 2.3→18.05 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.522 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 949 2.1 %RANDOM
Rwork0.165 ---
obs0.166 46268 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 210.92 Å2 / Biso mean: 49.847 Å2 / Biso min: 24.28 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→18.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6261 0 307 682 7250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0216767
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9889221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8825780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36324.295319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.292151053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5721538
X-RAY DIFFRACTIONr_chiral_restr0.0770.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025080
X-RAY DIFFRACTIONr_nbd_refined0.1860.23316
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24552
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2654
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.221
X-RAY DIFFRACTIONr_mcbond_it0.3751.54029
X-RAY DIFFRACTIONr_mcangle_it0.60926234
X-RAY DIFFRACTIONr_scbond_it1.05833222
X-RAY DIFFRACTIONr_scangle_it1.8284.52987
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3122 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.360.5
MEDIUM THERMAL0.322
LS refinement shellResolution: 2.3→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 73 -
Rwork0.215 3198 -
all-3271 -
obs--98.44 %

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