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- PDB-7kmp: Crystal structure of the GH31 alpha-xylosidase (Xac1773) from Xan... -

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Basic information

Entry
Database: PDB / ID: 7kmp
TitleCrystal structure of the GH31 alpha-xylosidase (Xac1773) from Xanthomonas citri
ComponentsAlpha-xylosidase
KeywordsHYDROLASE / Glycoside Hydrolase Family 31 / Xyloglucan
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Alpha-glucosidase, N-terminal / : / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / Glycoside hydrolase family 31 ...Alpha-glucosidase, N-terminal / : / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / Alpha-xylosidase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.556 Å
AuthorsVieira, P.S. / Murakami, M.T.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2016/06509-0 Brazil
Sao Paulo Research Foundation (FAPESP)2015/26982-0 Brazil
CitationJournal: Nature Communications / Year: 2021
Title: Xyloglucan processing machinery in Xanthomonas pathogens and its role in the transcriptional activation of virulence factors
Authors: Vieira, P.S. / Bonfim, I.M. / Araujo, E.A. / Melo, R.R. / Lima, A.R. / Fessel, M.R. / Paixao, D.A.A. / Persinoti, G.F. / Rocco, S.A. / Lima, T.B. / Pirolla, R.A.S. / Morais, M.A.B. / Correa, ...Authors: Vieira, P.S. / Bonfim, I.M. / Araujo, E.A. / Melo, R.R. / Lima, A.R. / Fessel, M.R. / Paixao, D.A.A. / Persinoti, G.F. / Rocco, S.A. / Lima, T.B. / Pirolla, R.A.S. / Morais, M.A.B. / Correa, J.B.L. / Zanphorlin, L.M. / Diogo, J.A. / Lima, E.A. / Grandis, A. / Buckeridge, M.S. / Gozzo, F.C. / Benedetti, C.E. / Polikarpov, I. / Giuseppe, P.O. / Murakami, M.T.
History
DepositionNov 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,28115
Polymers111,0451
Non-polymers1,23614
Water20,3931132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.450, 146.410, 63.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Alpha-xylosidase


Mass: 111044.625 Da / Num. of mol.: 1 / Mutation: A316V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria)
Strain: 306 / Gene: xylS, XAC1773 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8PLM2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1132 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 mol/L potassium nitrate 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4587 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 13, 2018
RadiationMonochromator: Water-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4587 Å / Relative weight: 1
ReflectionResolution: 1.55→45.807 Å / Num. obs: 155571 / % possible obs: 99.7 % / Redundancy: 9.71 % / CC1/2: 0.99 / Net I/σ(I): 20.15
Reflection shellResolution: 1.55→1.64 Å / Mean I/σ(I) obs: 6.96 / Num. unique obs: 24655 / CC1/2: 0.98 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIXdev_3139refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XVG

2xvg


Resolution: 1.556→45.807 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1854 7779 5 %
Rwork0.1616 147782 -
obs0.1628 155561 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.47 Å2 / Biso mean: 21.7408 Å2 / Biso min: 9.83 Å2
Refinement stepCycle: final / Resolution: 1.556→45.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7337 0 79 1132 8548
Biso mean--30.37 31.73 -
Num. residues----920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5565-1.57420.29122300.2717437589
1.5742-1.59270.23162580.19824896100
1.5927-1.61210.22672580.19384909100
1.6121-1.63250.22172560.18574850100
1.6325-1.6540.20822580.18044904100
1.654-1.67670.21482600.18424938100
1.6767-1.70060.20932570.17844892100
1.7006-1.7260.19042560.17514869100
1.726-1.7530.22892610.18194954100
1.753-1.78170.19452550.17844845100
1.7817-1.81240.2212600.17854934100
1.8124-1.84540.22772570.18154881100
1.8454-1.88090.20772590.1834914100
1.8809-1.91930.2142590.1784933100
1.9193-1.9610.19112610.17134946100
1.961-2.00660.19192550.17284853100
2.0066-2.05680.19262610.17534959100
2.0568-2.11240.22472600.17364940100
2.1124-2.17460.20112600.16974931100
2.1746-2.24480.18982580.16484918100
2.2448-2.3250.18692610.16744948100
2.325-2.41810.18792610.16814962100
2.4181-2.52810.18332600.1624945100
2.5281-2.66140.19312620.16674964100
2.6614-2.82810.20672610.16644966100
2.8281-3.04640.20062620.16394987100
3.0464-3.35290.17452650.15255022100
3.3529-3.83790.17062640.13935029100
3.8379-4.83450.12722680.12435090100
4.8345-45.8070.15882760.1517522899

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