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- PDB-3wf1: Crystal structure of human beta-galactosidase in complex with 6S-... -

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Basic information

Entry
Database: PDB / ID: 3wf1
TitleCrystal structure of human beta-galactosidase in complex with 6S-NBI-GJ
ComponentsBeta-galactosidase
KeywordsHYDROLASE / GLYCOSYL HYDROLASE / TIM-BARREL DOMAIN
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 / carbohydrate metabolic process / ficolin-1-rich granule lumen / 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-6GJ / Beta-galactosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSuzuki, H. / Ohto, U. / Shimizu, T.
CitationJournal: to be published
Title: Structural basis of pharmacological chaperoning for human beta-galactosidase
Authors: Suzuki, H. / Ohto, U. / Higaki, K. / Mena-Barragan, T. / Aguilar-Moncayo, M. / Ortiz Mellet, C. / Nanba, E. / Garcia Fernandez, J.M. / Suzuki, Y. / Shimizu, T.
History
DepositionJul 16, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 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 1.3Oct 30, 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)312,52544
Polymers306,4734
Non-polymers6,05240
Water28,7521596
1
A: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,26222
Polymers153,2372
Non-polymers3,02620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-51 kcal/mol
Surface area44650 Å2
MethodPISA
2
B: Beta-galactosidase
C: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,26222
Polymers153,2372
Non-polymers3,02620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-46 kcal/mol
Surface area44470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.912, 116.008, 140.569
Angle α, β, γ (deg.)90.00, 92.28, 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 / Acid beta-galactosidase / Lactase / Elastin receptor 1


Mass: 76618.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELNR1, GLB1 / 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, 1620 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-6GJ / (3E,5S,6R,7S,8S,8aS)-3-(butylimino)hexahydro[1,3]thiazolo[3,4-a]pyridine-5,6,7,8-tetrol


Mass: 276.353 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H20N2O4S
#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.: 1596 / 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: 53.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, Ammonium sulfate, pH 7.5, vapor diffusion, sittingdrop, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 199457 / % possible obs: 97.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.2 / % possible all: 96.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3THC

3thc


Resolution: 2→25.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.174 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 10030 5 %RANDOM
Rwork0.18585 ---
obs0.18821 189371 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.04 Å2 / Biso mean: 28.796 Å2 / Biso min: 13.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2→25.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19206 0 372 1596 21174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01920287
X-RAY DIFFRACTIONr_bond_other_d0.0010.0218736
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.97527674
X-RAY DIFFRACTIONr_angle_other_deg1.3043.00143104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02352410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16823.775914
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.867153095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6091598
X-RAY DIFFRACTIONr_chiral_restr0.1020.22982
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02122734
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024772
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 751 -
Rwork0.245 13671 -
all-14422 -
obs--95.92 %

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