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- PDB-3thd: Crystal structure of human beta-galactosidase in complex with 1-d... -

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Basic information

Entry
Database: PDB / ID: 3thd
TitleCrystal structure of human beta-galactosidase in complex with 1-deoxygalactonojirimycin
ComponentsBeta-galactosidase
KeywordsHYDROLASE / BETA-GALACTOSIDASE / TIM-BARREL DOMAIN / GLYCOSYL HYDROLASE / Glycosylation
Function / homology
Function and homology information


MPS IV - Morquio syndrome B (Keratin metabolism) / keratan sulfate proteoglycan catabolic process / response to cortisone / response to Thyroglobulin triiodothyronine / Defective NEU1 causes sialidosis / Keratan sulfate degradation / galactose catabolic process / Sialic acid metabolism / galactoside binding / heparan sulfate proteoglycan catabolic process ...MPS IV - Morquio syndrome B (Keratin metabolism) / keratan sulfate proteoglycan catabolic process / response to cortisone / response to Thyroglobulin triiodothyronine / Defective NEU1 causes sialidosis / Keratan sulfate degradation / galactose catabolic process / Sialic acid metabolism / galactoside binding / heparan sulfate proteoglycan catabolic process / glycosphingolipid catabolic process / HS-GAG degradation / glycoprotein catabolic process / Glycosphingolipid catabolism / beta-galactosidase / ganglioside catabolic process / vacuole / beta-galactosidase activity / lysosomal lumen / azurophil granule lumen / ficolin-1-rich granule lumen / carbohydrate metabolic process / lysosome / intracellular membrane-bounded organelle / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / membrane / cytoplasm
Similarity search - Function
Beta-galactosidase 1-like / : / Beta-galactosidase, first all-beta domain / : / Beta-galactosidase second all-beta domain / Beta-galactosidase, galactose-binding domain / Glycoside hydrolase, family 35, conserved site / Glycosyl hydrolases family 35 putative active site. / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 ...Beta-galactosidase 1-like / : / Beta-galactosidase, first all-beta domain / : / Beta-galactosidase second all-beta domain / Beta-galactosidase, galactose-binding domain / Glycoside hydrolase, family 35, conserved site / Glycosyl hydrolases family 35 putative active site. / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-DGJ / Beta-galactosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsOhto, U. / Shimizu, T.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of human beta-galactosidase: structural basis of Gm1 gangliosidosis and morquio B diseases
Authors: Ohto, U. / Usui, K. / Ochi, T. / Yuki, K. / Satow, Y. / Shimizu, T.
History
DepositionAug 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _struct_conn.ptnr1_label_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 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 1.4Nov 13, 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: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,26044
Polymers294,6614
Non-polymers5,59940
Water39,3452184
1
A: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,13022
Polymers147,3312
Non-polymers2,79920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-39 kcal/mol
Surface area44370 Å2
MethodPISA
2
B: Beta-galactosidase
C: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,13022
Polymers147,3312
Non-polymers2,79920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-38 kcal/mol
Surface area44440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.792, 115.996, 140.327
Angle α, β, γ (deg.)90.00, 92.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 20 molecules ABCD

#1: Protein
Beta-galactosidase


Mass: 73665.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLB1, ELNR1 / Production host: Pichia pastoris (fungus) / References: UniProt: P16278, beta-galactosidase
#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.: 16
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 , 5 types, 2208 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-DGJ / (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol / 1-deoxygalactonojirimycin


Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: Galafold, medication*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2184 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% (w/v) PEG3350 0.2M ammonium sulfate 100mM Tris HCl pH 8.0 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→29.29 Å / Num. obs: 249160

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D3A

3d3a


Resolution: 1.79→29.29 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.008 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22796 13274 5.1 %RANDOM
Rwork0.19752 ---
obs0.19906 249160 92.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.053 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.02 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.79→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19198 0 344 2184 21726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0220421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.97327915
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43252468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96223.835910
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.836153094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4441594
X-RAY DIFFRACTIONr_chiral_restr0.180.23016
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115859
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.794→1.841 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 826 -
Rwork0.261 15403 -
obs--78.93 %
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)
10.3670.0177-0.00150.18420.01670.2169-0.0150.0351-0.004-0.01620.010.01320.00240.00540.0050.05440.0006-0.02410.0477-0.00390.02230.1540.58113.732
21.9145-2.26710.25144.47171.9172.9187-0.2069-0.2613-0.19790.31570.04120.35680.0641-0.25340.16570.04810.01190.00910.15150.04110.0572-3.676-2.63139.671
30.3628-0.05270.11310.3426-0.0650.3731-0.01910.06680.0508-0.03930.0209-0.0058-0.0078-0.0091-0.00180.0638-0.00460.0060.05740.01670.024537.06421.5524.504
40.5496-0.237-0.07710.24780.17780.246-0.0219-0.0389-0.02080.05020.038-0.02390.0370.0104-0.01620.06290.0103-0.00260.0467-0.00570.030547.6714.7727.645
50.4159-0.0654-0.05460.12980.0920.5884-0.0032-0.06550.00330.0288-0.0079-0.01870.0199-0.01720.0110.05520.0034-0.00450.1013-0.03080.0169.55928.91261.966
60.4498-0.2614-0.25480.2611-0.10050.79330.06920.09960.02780.01140.0022-0.0069-0.1769-0.1637-0.07140.08660.06210.01310.08760.00040.01860.07846.53739.097
70.447-0.10920.07770.1731-0.10320.5652-0.0167-0.0742-0.01280.03160.01510.0384-0.02070.0280.00160.04990-0.0040.10350.03330.022632.444-15.761.046
80.8158-0.4350.31480.2691-0.0260.8040.10220.1349-0.0981-0.0277-0.03030.05870.18250.1859-0.07190.08440.0596-0.03690.0837-0.00570.04142.051-32.78337.716
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 625
2X-RAY DIFFRACTION2A626 - 647
3X-RAY DIFFRACTION3B29 - 357
4X-RAY DIFFRACTION4B358 - 647
5X-RAY DIFFRACTION5C29 - 357
6X-RAY DIFFRACTION6C358 - 647
7X-RAY DIFFRACTION7D29 - 357
8X-RAY DIFFRACTION8D358 - 647

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