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- PDB-7kmm: Crystal structure of XAC1771, a novel carbohydrate acetylesterase... -

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Basic information

Entry
Database: PDB / ID: 7kmm
TitleCrystal structure of XAC1771, a novel carbohydrate acetylesterase from Xanthomonas citri
ComponentsSialic acid-specific 9-O-acetylesterase
KeywordsHYDROLASE / Carbohydrate esterase / SGNH-hydrolase / Xyloglucan / GDSL-like esterase
Function / homologySialate O-acetylesterase / Sialate O-acetylesterase domain / Carbohydrate esterase, sialic acid-specific acetylesterase / Beta-galactosidase jelly roll domain / Beta-galactosidase second all-beta domain / sialate O-acetylesterase activity / SGNH hydrolase superfamily / Galactose-binding-like domain superfamily / Sialic acid-specific 9-O-acetylesterase
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.899 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialic acid-specific 9-O-acetylesterase
B: Sialic acid-specific 9-O-acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,27215
Polymers137,4222
Non-polymers85013
Water6,864381
1
A: Sialic acid-specific 9-O-acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1698
Polymers68,7111
Non-polymers4587
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sialic acid-specific 9-O-acetylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1037
Polymers68,7111
Non-polymers3926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.852, 63.497, 88.284
Angle α, β, γ (deg.)90.000, 98.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sialic acid-specific 9-O-acetylesterase


Mass: 68710.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria)
Strain: 306 / Gene: XAC1771 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8PLM4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 1.58 Å3/Da / Density % sol: 21.92 % / Description: Small plates
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 mol/L Tris 20% PEG 6000 0.01 mol/L Zinc chloride

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.899→19.97 Å / Num. obs: 126243 / % possible obs: 95.6 % / Redundancy: 7.133 % / CC1/2: 0.998 / Net I/σ(I): 12.01
Reflection shellResolution: 1.899→2.01 Å / Mean I/σ(I) obs: 1.36 / Num. unique obs: 20260 / CC1/2: 0.617 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIXdev_3139refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
SHELXSphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.899→19.97 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 3064 4.93 %
Rwork0.1897 59142 -
obs0.1921 62206 92.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.83 Å2 / Biso mean: 26.5948 Å2 / Biso min: 11.52 Å2
Refinement stepCycle: final / Resolution: 1.899→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6607 0 13 381 7001
Biso mean--54.02 28.59 -
Num. residues----867
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8994-1.92910.33511060.3161223576
1.9291-1.96070.36731310.2923237382
1.9607-1.99440.29481250.2845237282
1.9944-2.03070.28481340.2648242184
2.0307-2.06970.33571270.2579240683
2.0697-2.11190.33761330.2254253387
2.1119-2.15780.24791440.2156256289
2.1578-2.20790.2531280.2083266191
2.2079-2.2630.26691360.2114266191
2.263-2.32410.30481450.2062266792
2.3241-2.39240.26191470.1943266792
2.3924-2.46950.24931280.2026274494
2.4695-2.55760.2451570.1918274295
2.5576-2.65980.25481380.1894282696
2.6598-2.78050.25831320.2008284497
2.7805-2.92670.24151640.1961282298
2.9267-3.10940.26871520.2039286299
3.1094-3.34850.21831450.1837291699
3.3485-3.68350.20981450.1642292699
3.6835-4.21220.19641450.15012945100
4.2122-5.29060.18921470.15812945100
5.2906-19.970.20591550.1753012100

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