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- PDB-9fz9: Glycoside Hydrolase Family 157 from Labilibaculum antarcticum, wi... -

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Basic information

Entry
Database: PDB / ID: 9fz9
TitleGlycoside Hydrolase Family 157 from Labilibaculum antarcticum, wild type SeMet derivative (LaGH157)
ComponentsGlycoside hydrolase family 2 catalytic domain-containing protein
KeywordsHYDROLASE / GH157 / endo-1 / 3(4)-beta-glucanase / Labilibaculum antarcticum / Wild type SeMet derivative
Function / homologyGlycoside hydrolase superfamily / ACETATE ION / MALONIC ACID / Glycoside hydrolase family 2 catalytic domain-containing protein
Function and homology information
Biological speciesLabilibaculum antarcticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.443 Å
AuthorsBule, P. / Alves, V.D. / Carvalho, A.L.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaUIDB/00276/2020, LA/P/0059/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/04378/2020, UIDB/04378/2020, LA/P/0140/2020 Portugal
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Family GH157 enzyme exhibits broad linkage tolerance and a dual endo/exo-beta-glucanase activity on beta-glucans.
Authors: Caseiro, C. / McGregor, N.G.S. / Alves, V.D. / Carvalho, A.L. / Romao, M.J. / Davies, G.J. / Fontes, C.M.G.A. / Bule, P.
History
DepositionJul 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 2 catalytic domain-containing protein
B: Glycoside hydrolase family 2 catalytic domain-containing protein
C: Glycoside hydrolase family 2 catalytic domain-containing protein
D: Glycoside hydrolase family 2 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,86511
Polymers248,3074
Non-polymers5577
Water6,792377
1
A: Glycoside hydrolase family 2 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4506
Polymers62,0771
Non-polymers3735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 2 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2613
Polymers62,0771
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoside hydrolase family 2 catalytic domain-containing protein


Theoretical massNumber of molelcules
Total (without water)62,0771
Polymers62,0771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoside hydrolase family 2 catalytic domain-containing protein


Theoretical massNumber of molelcules
Total (without water)62,0771
Polymers62,0771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.154, 112.582, 251.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glycoside hydrolase family 2 catalytic domain-containing protein


Mass: 62076.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Labilibaculum antarcticum (bacteria) / Gene: ALGA_4297 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y1CQ89
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 4% (v/v) tacsimate pH 6.0, 12% (w/v) PolyEthylene Glycol 3,350 (PEG 3350)
PH range: 4.0-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.44→49.41 Å / Num. obs: 102074 / % possible obs: 93.7 % / Redundancy: 10.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.039 / Rrim(I) all: 0.134 / Χ2: 0.91 / Net I/σ(I): 14.5 / Num. measured all: 1105365
Reflection shellResolution: 2.44→2.53 Å / % possible obs: 65.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 1.018 / Num. measured all: 35632 / Num. unique obs: 6816 / CC1/2: 0.54 / Rpim(I) all: 0.474 / Rrim(I) all: 1.13 / Χ2: 0.68 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
AutoSolphasing
xia2data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.443→49.41 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.262 --
Rwork0.249 --
obs-96991 93.5 %
Refinement stepCycle: LAST / Resolution: 2.443→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16987 0 37 377 17401

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