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- PDB-8qme: Structural characterization of beta-xyloxidase XynB2 from Geobaci... -

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Basic information

Entry
Database: PDB / ID: 8qme
TitleStructural characterization of beta-xyloxidase XynB2 from Geobacillus stearothermophilus CECT43
ComponentsBeta-xylosidase
KeywordsHYDROLASE / BETA-XYLOSIDASE
Function / homologyGlycoside hydrolase, family 52 / Glycosyl hydrolase family 52 / xylan 1,4-beta-xylosidase activity / : / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / carbohydrate metabolic process / ACETATE ION / Beta-xylosidase
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGavira, J.A. / Martinez-Rodriguez, S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-116261GB-I00 Spain
CitationJournal: Crystals / Year: 2024
Title: Structural Characterization of beta-Xylosidase XynB2 from Geobacillus stearothermophilus CECT43: A Member of the Glycoside Hydrolase Family GH52
Authors: Gavira, J.A. / Contreras, L.M. / Alshamaa, H.M. / Clemente-Jimenez, J.M. / Rodriguez-Vico, F. / Las Heras-Vazquez, F.J. / Martinez-Rodriguez, S.
History
DepositionSep 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-xylosidase
B: Beta-xylosidase
C: Beta-xylosidase
D: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,74135
Polymers322,9914
Non-polymers2,74931
Water26,7881487
1
A: Beta-xylosidase
B: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,83917
Polymers161,4962
Non-polymers1,34315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-113 kcal/mol
Surface area43300 Å2
MethodPISA
2
C: Beta-xylosidase
D: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,90218
Polymers161,4962
Non-polymers1,40616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-119 kcal/mol
Surface area43750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.121, 97.514, 107.400
Angle α, β, γ (deg.)107.45, 98.48, 106.55
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-xylosidase


Mass: 80747.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: GA8_03270 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9HVH2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1487 / 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: 49 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 5 / Details: Sodium Acetate 0.1M pH 5.0, Ammonium Sulphate 2.8M / PH range: 3.0-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.25→99.08 Å / Num. obs: 134250 / % possible obs: 97.2 % / Redundancy: 1.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.1 / Rrim(I) all: 0.141 / Χ2: 0.49 / Net I/σ(I): 3.6 / Num. measured all: 235632
Reflection shellResolution: 2.25→2.29 Å / % possible obs: 95.7 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.59 / Num. measured all: 11351 / Num. unique obs: 6524 / CC1/2: 0.558 / Rpim(I) all: 0.59 / Rrim(I) all: 0.835 / Χ2: 0.48 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RHH

4rhh


Resolution: 2.25→81.67 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 6751 5.03 %
Rwork0.1777 --
obs0.1795 134215 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→81.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21815 0 161 1492 23468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.554
X-RAY DIFFRACTIONf_dihedral_angle_d6.0453133
X-RAY DIFFRACTIONf_chiral_restr0.0413277
X-RAY DIFFRACTIONf_plane_restr0.0054050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.33062180.31364180X-RAY DIFFRACTION95
2.28-2.30.31812230.28084191X-RAY DIFFRACTION96
2.3-2.330.29882100.26894269X-RAY DIFFRACTION97
2.33-2.360.27191820.25514199X-RAY DIFFRACTION97
2.36-2.390.29082330.25744334X-RAY DIFFRACTION97
2.39-2.420.29421990.26254150X-RAY DIFFRACTION97
2.42-2.460.30222310.2534212X-RAY DIFFRACTION96
2.46-2.50.28472080.24454314X-RAY DIFFRACTION97
2.5-2.530.27742210.23234157X-RAY DIFFRACTION95
2.53-2.580.2752260.21654192X-RAY DIFFRACTION97
2.58-2.620.27822060.21034286X-RAY DIFFRACTION96
2.62-2.670.24322190.20974208X-RAY DIFFRACTION97
2.67-2.720.26652180.21324262X-RAY DIFFRACTION97
2.72-2.770.25432080.19994282X-RAY DIFFRACTION98
2.77-2.830.22772600.20274261X-RAY DIFFRACTION97
2.83-2.90.24232490.20444237X-RAY DIFFRACTION97
2.9-2.970.27152470.20944225X-RAY DIFFRACTION98
2.97-3.050.2452230.19684266X-RAY DIFFRACTION97
3.05-3.140.22072490.18484241X-RAY DIFFRACTION98
3.14-3.250.23191920.17684282X-RAY DIFFRACTION97
3.25-3.360.20272080.17024283X-RAY DIFFRACTION97
3.36-3.50.22162590.1624245X-RAY DIFFRACTION98
3.5-3.650.19452010.15734308X-RAY DIFFRACTION98
3.65-3.850.1692400.13854314X-RAY DIFFRACTION98
3.85-4.090.16412390.13074277X-RAY DIFFRACTION99
4.09-4.40.16012250.1294270X-RAY DIFFRACTION98
4.4-4.850.14922260.12214223X-RAY DIFFRACTION96
4.85-5.550.162400.13214282X-RAY DIFFRACTION99
5.55-6.990.18642340.16294310X-RAY DIFFRACTION98
6.99-81.670.18052570.16444204X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.60810.1671-0.26450.2829-0.17460.5788-0.0448-0.0473-0.08790.0270.0009-0.03620.04130.0239-0.00010.2280.0401-0.00210.1660.00860.22530.38360.41030.5289
20.80080.1905-0.3740.3531-0.16720.4933-0.11150.1882-0.1012-0.05320.053-0.06360.1149-0.0764-0.00520.2143-0.01680.01450.2004-0.04320.187417.638610.6976-43.1819
30.55380.13650.34490.29550.22021.0973-0.0314-0.02380.04620.04940.03610.0047-0.06580.0029-0.00040.19020.0344-0.00310.1510.00870.195-24.393811.992896.8594
40.4882-0.01290.26660.23320.09140.857-0.00820.02350.068-0.03220.0268-0.0317-0.18960.09030.00030.2366-0.03210.02580.2040.02450.2112-20.740817.579748.9795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 705)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 704)
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 704)
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 705)

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