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- PDB-7kmn: Crystal structure of XAC1772, a GH35 xyloglucan-active beta-galac... -

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Basic information

Entry
Database: PDB / ID: 7kmn
TitleCrystal structure of XAC1772, a GH35 xyloglucan-active beta-galactosidase from Xanthomonas citri
ComponentsBeta-galactosidase, GH35 family
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
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.1Jun 16, 2021Group: Derived calculations / Category: pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation ..._pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2]
Revision 1.2Jul 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 1.3Oct 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 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0295
Polymers59,6451
Non-polymers3844
Water9,368520
1
A: Beta-galactosidase, GH35 family
hetero molecules

A: Beta-galactosidase, GH35 family
hetero molecules

A: Beta-galactosidase, GH35 family
hetero molecules

A: Beta-galactosidase, GH35 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,11720
Polymers238,5804
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Unit cell
Length a, b, c (Å)115.820, 115.820, 97.220
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 family


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


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 mol/L lithium sulfate 1.26 mol/L ammonium sulfate 0.1 mol/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: 1.45873 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: 1.45873 Å / Relative weight: 1
ReflectionResolution: 1.8→19.863 Å / Num. obs: 59344 / % possible obs: 100 % / Redundancy: 6.582 % / CC1/2: 0.999 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 0.85 / Num. unique obs: 9526 / CC1/2: 0.376 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_3139refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D1I

4d1i


Resolution: 1.8→19.863 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 2964 5 %
Rwork0.1769 56324 -
obs0.1786 59288 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.33 Å2 / Biso mean: 32.2155 Å2 / Biso min: 18.53 Å2
Refinement stepCycle: final / Resolution: 1.8→19.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 20 520 4580
Biso mean--62.94 36.83 -
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 (%)
1.8-1.82930.37321400.353264199
1.8293-1.86080.33671390.31892670100
1.8608-1.89460.3291410.29872675100
1.8946-1.9310.29781400.29542664100
1.931-1.97040.31051410.25942681100
1.9704-2.01320.28561400.24282662100
2.0132-2.060.27791410.2232663100
2.06-2.11140.2521420.20862712100
2.1114-2.16850.24721400.19922646100
2.1685-2.23220.25531400.19552676100
2.2322-2.30410.25541420.21322685100
2.3041-2.38640.22271410.18692685100
2.3864-2.48170.22481400.18432656100
2.4817-2.59450.21991420.17672695100
2.5945-2.73090.22811420.17912697100
2.7309-2.90150.24271410.18412678100
2.9015-3.12480.21811410.19162689100
3.1248-3.43780.19381430.16872707100
3.4378-3.93190.15221410.14372681100
3.9319-4.94110.15851420.12012711100
4.9411-19.8630.17461450.1492750100

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