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- PDB-8puo: Structural determinants of cold-activity and glucose tolerance of... -

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Basic information

Entry
Database: PDB / ID: 8puo
TitleStructural determinants of cold-activity and glucose tolerance of a family 1 glycoside hydrolase (GH1) from Antarctic Marinomonas Ef 1
ComponentsBeta-glucosidase
KeywordsHYDROLASE / cold-active enzymes / GH1 family / psychrophiles / glucose-tolerance
Function / homology
Function and homology information


: / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesMarinomonas sp. ef1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGourlay, L.J. / Nardini, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2024
Title: Structural determinants of cold activity and glucose tolerance of a family 1 glycoside hydrolase (GH1) from Antarctic Marinomonas sp. ef1.
Authors: Gourlay, L.J. / Mangiagalli, M. / Moroni, E. / Lotti, M. / Nardini, M.
History
DepositionJul 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucosidase
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,36328
Polymers103,6292
Non-polymers1,73426
Water11,259625
1
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,68114
Polymers51,8141
Non-polymers86713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,68114
Polymers51,8141
Non-polymers86713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.116, 201.120, 47.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Beta-glucosidase


Mass: 51814.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas sp. ef1 (bacteria) / Gene: TY87_18135 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2M8K1U8, beta-glucosidase
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: M-GH1 crystals grew over 2-4 days in 50% protein drop in an optimized condition of PACT condition G1, containing 22% (w/v) PEG 3500, 0.1 M sodium fluoride (NaF) and 0.1 M Tris-HCl pH 8.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.8→67 Å / Num. obs: 91533 / % possible obs: 98.3 % / Redundancy: 10.7 % / Biso Wilson estimate: 20.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.087 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12892 / CC1/2: 0.805 / Rrim(I) all: 1.038 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.88 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 1997 2.19 %
Rwork0.1648 --
obs0.1653 91394 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7119 0 112 625 7856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0187403
X-RAY DIFFRACTIONf_angle_d1.2710009
X-RAY DIFFRACTIONf_dihedral_angle_d14.3172681
X-RAY DIFFRACTIONf_chiral_restr0.0831063
X-RAY DIFFRACTIONf_plane_restr0.011293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.31721380.26836168X-RAY DIFFRACTION95
1.85-1.890.29821370.23686137X-RAY DIFFRACTION96
1.89-1.950.29761380.24646169X-RAY DIFFRACTION96
1.95-2.010.26371410.21846290X-RAY DIFFRACTION97
2.01-2.090.23861380.19716279X-RAY DIFFRACTION98
2.09-2.170.21661410.18646318X-RAY DIFFRACTION98
2.17-2.270.19271420.17496383X-RAY DIFFRACTION98
2.27-2.390.21731440.17946392X-RAY DIFFRACTION99
2.39-2.540.20411360.16866124X-RAY DIFFRACTION95
2.54-2.730.18361450.16776464X-RAY DIFFRACTION100
2.73-3.010.19471480.16486570X-RAY DIFFRACTION100
3.01-3.440.19051470.15676586X-RAY DIFFRACTION100
3.44-4.340.14411480.13396626X-RAY DIFFRACTION100
4.34-45.880.15431540.14216891X-RAY DIFFRACTION100

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