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- PDB-7kmo: Crystal structure of the GH35 beta-galactosidase (Xac1772) from X... -

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Basic information

Entry
Database: PDB / ID: 7kmo
TitleCrystal structure of the GH35 beta-galactosidase (Xac1772) from Xanthomonas citri in complex with galactose
ComponentsBeta-galactosidase, GH35
KeywordsHYDROLASE / Glycoside Hydrolase Family 35 / Xyloglucan
Function / homology
Function and homology information


beta-galactosidase complex / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Domain of unknown function DUF5597 / Domain of unknown function (DUF5597) / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Glycoside hydrolase, family 35 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-D-galactopyranose / Glycoside hydrolase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.753 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: Beta-galactosidase, GH35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4789
Polymers59,6451
Non-polymers8338
Water9,116506
1
A: Beta-galactosidase, GH35
hetero molecules

A: Beta-galactosidase, GH35
hetero molecules

A: Beta-galactosidase, GH35
hetero molecules

A: Beta-galactosidase, GH35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,91136
Polymers238,5804
Non-polymers3,33132
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area15750 Å2
ΔGint-50 kcal/mol
Surface area73810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.680, 116.680, 97.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Beta-galactosidase, GH35 /


Mass: 59644.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria)
Strain: 306 / Gene: XAC1772 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8PLM3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2 mol/L ammonium sulfate 8% glycerol 0.1 mmol/L tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45872 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: 1.45872 Å / Relative weight: 1
ReflectionResolution: 1.75→19.447 Å / Num. obs: 63855 / % possible obs: 97.4 % / Redundancy: 6.47 % / CC1/2: 0.998 / Net I/σ(I): 8.92
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 5.958 % / Mean I/σ(I) obs: 0.64 / Num. unique obs: 10477 / CC1/2: 0.327 / % possible all: 99.8

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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: 4D1I

4d1i


Resolution: 1.753→19.447 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2415 3038 5 %
Rwork0.1934 57714 -
obs0.1958 60752 92.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.91 Å2 / Biso mean: 37.8966 Å2 / Biso min: 23.77 Å2
Refinement stepCycle: final / Resolution: 1.753→19.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 52 506 4598
Biso mean--60.9 41.87 -
Num. residues----511
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.753-1.78020.35361450.3432276199
1.7802-1.80940.38111490.35152845100
1.8094-1.84050.38071470.34012800100
1.8405-1.8740.37491430.3749269896
1.874-1.910.7148800.6401153192
1.91-1.94890.603560.4749107942
1.9489-1.99130.31421470.27982792100
1.9913-2.03760.29341490.22862830100
2.0376-2.08850.25071490.21572821100
2.0885-2.14490.25431480.22792814100
2.1449-2.20790.25341480.23212811100
2.2079-2.2790.6383930.5471173861
2.279-2.36040.31241380.2462616100
2.3604-2.45470.29361500.2052854100
2.4547-2.56620.24831470.18942793100
2.5662-2.70110.22241490.17732829100
2.7011-2.86990.22431510.18212860100
2.8699-3.09070.23881490.18082833100
3.0907-3.40020.20381490.1692842100
3.4002-3.88880.23251490.1596281899
3.8888-4.88660.14711500.12362849100
4.8866-19.4470.1751520.13862900100

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