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- PDB-6m4e: Crystal structure of a GH1 beta-glucosidase from Hamamotoa singularis -

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Basic information

Entry
Database: PDB / ID: 6m4e
TitleCrystal structure of a GH1 beta-glucosidase from Hamamotoa singularis
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: 2.1 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 6, 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 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,67161
Polymers64,3461
Non-polymers5,32460
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint140 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.790, 172.830, 67.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-835-

HOH

21A-945-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 64346.238 Da / Num. of mol.: 1
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

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Sugars , 3 types, 7 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.: 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
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
#4: 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.: 1
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 , 2 types, 224 molecules

#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 53 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.63 Å3/Da / Density % sol: 66.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M MIB Buffer pH 7.0, 25% (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 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→44.29 Å / Num. obs: 55035 / % possible obs: 99.9 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.95
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 13 % / Rmerge(I) obs: 1.775 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 5423 / % possible all: 99.9

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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: 2.1→39.24 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 2751 5 %
Rwork0.174 --
obs0.175 55019 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 343 171 4802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.33211350.30032567X-RAY DIFFRACTION100
2.14-2.180.31651360.27852582X-RAY DIFFRACTION100
2.18-2.220.29111350.25162559X-RAY DIFFRACTION100
2.22-2.260.31370.25642603X-RAY DIFFRACTION100
2.26-2.310.26181360.22722600X-RAY DIFFRACTION100
2.31-2.370.23031360.20622567X-RAY DIFFRACTION100
2.37-2.420.19761360.19652590X-RAY DIFFRACTION100
2.42-2.490.20711360.18192593X-RAY DIFFRACTION100
2.49-2.560.22121380.18162610X-RAY DIFFRACTION100
2.56-2.650.22361350.18032565X-RAY DIFFRACTION100
2.65-2.740.21031370.18142610X-RAY DIFFRACTION100
2.74-2.850.20381370.17532601X-RAY DIFFRACTION100
2.85-2.980.19521370.16912605X-RAY DIFFRACTION100
2.98-3.140.20591380.17332609X-RAY DIFFRACTION100
3.14-3.330.20761370.16952621X-RAY DIFFRACTION100
3.33-3.590.18281390.16362627X-RAY DIFFRACTION100
3.59-3.950.1761390.16662647X-RAY DIFFRACTION100
3.95-4.520.16331390.14932646X-RAY DIFFRACTION100
4.52-5.690.18761410.15872676X-RAY DIFFRACTION100
5.69-39.240.18751470.17492789X-RAY DIFFRACTION100

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