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- PDB-3lrm: Structure of alfa-galactosidase from Saccharomyces cerevisiae wit... -

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Basic information

Entry
Database: PDB / ID: 3lrm
TitleStructure of alfa-galactosidase from Saccharomyces cerevisiae with raffinose
ComponentsAlpha-galactosidase 1
KeywordsHYDROLASE / alpha-galactosidase / Tetramer / GH27 / raffinose / Glycoprotein / Glycosidase
Function / homology
Function and homology information


alpha-galactosidase / alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / extracellular region / cytoplasm
Similarity search - Function
Glycoside hydrolase, melibiase / 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 ...Glycoside hydrolase, melibiase / 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 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsFernandez-Leiro, R. / Pereira-Rodriguez, A. / Cerdan, M.E. / Becerra, M. / Sanz-Aparicio, J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural analysis of Saccharomyces cerevisiae alpha-galactosidase and its complexes with natural substrates reveals new insights into substrate specificity of GH27 glycosidases.
Authors: Fernandez-Leiro, R. / Pereira-Rodriguez, A. / Cerdan, M.E. / Becerra, M. / Sanz-Aparicio, J.
History
DepositionFeb 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / 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 / pdbx_validate_chiral / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-galactosidase 1
B: Alpha-galactosidase 1
C: Alpha-galactosidase 1
D: Alpha-galactosidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,89023
Polymers212,3344
Non-polymers6,55519
Water18,4111022
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20200 Å2
ΔGint63 kcal/mol
Surface area61470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.170, 129.530, 136.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A19 - 470
2111B19 - 470
3111C19 - 470
4111D19 - 470

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Components

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Protein / Non-polymers , 2 types, 1026 molecules ABCD

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


Mass: 53083.621 Da / Num. of mol.: 4 / Mutation: D149A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MEL1 / Plasmid: YEPFLAG1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04824, alpha-galactosidase
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1022 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 19 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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.: 3
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
#4: Polysaccharide
beta-D-fructofuranose-(2-1)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb2-1[DGalpa1-6]DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#5: 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.: 9
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Deglycosylated sample. 19% PEG3350, 0.1 M BisTris, 0.2 M SCNK, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0722 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.7→94.05 Å / Num. obs: 54965 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 59 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 8.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 4.9 / Num. unique all: 7932 / Rsym value: 0.438 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
MOLREPphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→94.05 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.851 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.888 / SU ML: 0.324 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2781 5.1 %RANDOM
Rwork0.241 ---
obs0.243 54890 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 266.18 Å2 / Biso mean: 40.553 Å2 / Biso min: 4.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.7→94.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14060 0 430 1022 15512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02114889
X-RAY DIFFRACTIONr_angle_refined_deg1.0571.96620247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.03551804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78724.749716
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52152236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9621568
X-RAY DIFFRACTIONr_chiral_restr0.0660.22170
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111516
X-RAY DIFFRACTIONr_mcbond_it0.1791.58924
X-RAY DIFFRACTIONr_mcangle_it0.36214240
X-RAY DIFFRACTIONr_scbond_it0.62535965
X-RAY DIFFRACTIONr_scangle_it1.0884.56007
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3515 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ATIGHT POSITIONAL0.020.05
BTIGHT POSITIONAL0.020.05
CTIGHT POSITIONAL0.040.05
DTIGHT POSITIONAL0.020.05
ATIGHT THERMAL0.040.5
BTIGHT THERMAL0.040.5
CTIGHT THERMAL0.040.5
DTIGHT THERMAL0.040.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 190 -
Rwork0.344 3813 -
all-4003 -
obs--100 %

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