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- PDB-1szn: THE STRUCTURE OF ALPHA-GALACTOSIDASE -

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Basic information

Entry
Database: PDB / ID: 1szn
TitleTHE STRUCTURE OF ALPHA-GALACTOSIDASE
Componentsalpha-galactosidase
KeywordsHYDROLASE / (beta/alpha)8 barrel / two domains / glycoprotein
Function / homology
Function and homology information


alpha-galactosidase / alpha-galactosidase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase 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, C-terminal beta sandwich domain / Alpha galactosidase 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-galactosidase
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.54 Å
AuthorsGolubev, A.M. / Nagem, R.A.P. / Brando Neto, J.R. / Neustroev, K.N. / Eneyskaya, E.V. / Kulminskaya, A.A. / Shabalin, K.A. / Savel'ev, A.N. / Polikarpov, I.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of alpha-galactosidase from Trichoderma reesei and its complex with galactose: implications for catalytic mechanism.
Authors: Golubev, A.M. / Nagem, R.A.P. / Neustroev, K.N. / Eneyskaya, E.V. / Kulminskaya, A.A. / Shabalin, K.A. / Savel'ev, A.N. / Polikarpov, I.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of alpha-galactosidase from Trichoderma reesei.
Authors: Golubev, A.M. / Neustroev, K.N.
History
DepositionApr 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
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 / 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_validate_close_contact / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE Leu37, Pro70, Ala72, Ala88, Asn148, Phe151, Lys153, Thr161, Asp165, Thr167, Gly185, ...SEQUENCE Leu37, Pro70, Ala72, Ala88, Asn148, Phe151, Lys153, Thr161, Asp165, Thr167, Gly185, His196, Met202, Gln207, Ser216, Asp225, Asn230, Arg236, Leu238, Leu240, Leu245, Asp249, Met258, Asn297, Asn300, Ile327, Val335, Tyr337, Phe341, Val355, Ile360, Ala362, Thr363, Asn369, His378, Ser386, Asp389, Ala398, Gln415, Arg416 differ from the sequence database. These residues were used on the basis of the electron density map. The difference may be due to the use of different strains of Trichoderma reesei for sequencing and for the X-ray structure.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9527
Polymers45,6111
Non-polymers3,3416
Water11,223623
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.489, 79.054, 119.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

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Protein , 1 types, 1 molecules A

#1: Protein alpha-galactosidase


Mass: 45610.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hypocrea jecorina (fungus)
References: GenBank: 1580816, UniProt: Q92456*PLUS, alpha-galactosidase

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Sugars , 3 types, 4 molecules

#2: 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.: 2
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
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d3-e1_f3-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-2/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 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]{[(6+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 625 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.03 Å3/Da / Density % sol: 38.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, potassium phosphate, sodium phosphate , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 20, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→65 Å / Num. all: 65585 / Num. obs: 65481 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.074 / Net I/σ(I): 12.5
Reflection shellResolution: 1.54→1.56 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.475 / % possible all: 89.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.54→12 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.073 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18252 3191 5.1 %RANDOM
Rwork0.15119 ---
all0.177 62917 --
obs0.15282 59691 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.947 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2--0.03 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.54→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 223 623 4059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213545
X-RAY DIFFRACTIONr_bond_other_d0.0010.022989
X-RAY DIFFRACTIONr_angle_refined_deg1.861.9984862
X-RAY DIFFRACTIONr_angle_other_deg2.93636931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2683416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43315521
X-RAY DIFFRACTIONr_chiral_restr0.2130.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023784
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02663
X-RAY DIFFRACTIONr_nbd_refined0.2190.3724
X-RAY DIFFRACTIONr_nbd_other0.1950.32919
X-RAY DIFFRACTIONr_nbtor_other0.5780.511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.5452
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.540
X-RAY DIFFRACTIONr_mcbond_it0.9871.52069
X-RAY DIFFRACTIONr_mcangle_it1.58723312
X-RAY DIFFRACTIONr_scbond_it2.55831476
X-RAY DIFFRACTIONr_scangle_it3.7054.51550
LS refinement shellResolution: 1.543→1.582 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.402 204
Rwork0.335 3925
obs-3925

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