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- PDB-6m55: Crystal structure of the E496A mutant of HsBglA in complex with 4... -

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Basic information

Entry
Database: PDB / ID: 6m55
TitleCrystal structure of the E496A mutant of HsBglA in complex with 4-galactosyllactose
ComponentsBeta-galactosidase-like enzyme
KeywordsHYDROLASE / galactooligosaccharide / transgalactosylation / beta-galactosidase / beta-glucosidase / Hamamotoa singularis / STRUCTURAL PROTEIN
Function / homology
Function and homology information


beta-glucosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Beta-galactosidase-like enzyme
Similarity search - Component
Biological speciesHamamotoa singularis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsUehara, R. / Iwamoto, R. / Aoki, S. / Yoshizawa, T. / Takano, K. / Matsumura, H. / Tanaka, S.-i.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)18K05445 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H05401 Japan
CitationJournal: Protein Sci. / Year: 2020
Title: Crystal structure of a GH1 beta-glucosidase from Hamamotoa singularis.
Authors: Uehara, R. / Iwamoto, R. / Aoki, S. / Yoshizawa, T. / Takano, K. / Matsumura, H. / Tanaka, S.I.
History
DepositionMar 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase-like enzyme
D: Beta-galactosidase-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,00912
Polymers120,9062
Non-polymers3,10310
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint33 kcal/mol
Surface area37320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.686, 67.116, 117.585
Angle α, β, γ (deg.)90.000, 128.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Non-polymers , 2 types, 5 molecules AD

#1: Protein Beta-galactosidase-like enzyme / GH1 beta-glucosidase


Mass: 60452.949 Da / Num. of mol.: 2 / Mutation: E496A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hamamotoa singularis (fungus) / Gene: bglA / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: Q564N5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 10 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][b-D-Galp]{}}}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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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.: 4
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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Details

Has ligand of interestY
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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M SPG Buffer pH 7.0, 27% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→45.99 Å / Num. obs: 24658 / % possible obs: 96.66 % / Redundancy: 6.1 % / Biso Wilson estimate: 57.01 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1612 / Rpim(I) all: 0.06944 / Rrim(I) all: 0.1759 / Net I/σ(I): 7.27
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.5642 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 1795 / CC1/2: 0.912 / Rpim(I) all: 0.2658 / Rrim(I) all: 0.6255 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GXP

4gxp


Resolution: 3→45.21 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 34.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 1108 5 %
Rwork0.265 21034 -
obs0.266 22151 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.8 Å2 / Biso mean: 55.3936 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8568 0 202 3 8773
Biso mean--52.18 54.38 -
Num. residues----1084
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.140.46071390.42752643278299
3.14-3.30.38581400.35812654279498
3.3-3.510.34971380.31152615275397
3.51-3.780.34421370.27262608274596
3.78-4.160.28281350.24342560269595
4.16-4.760.30021350.23142562269795
4.76-60.26041390.23762637277697
6-45.210.2261450.21982755290098

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