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- PDB-7kn8: Crystal structure of the GH74 xyloglucanase from Xanthomonas camp... -

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Basic information

Entry
Database: PDB / ID: 7kn8
TitleCrystal structure of the GH74 xyloglucanase from Xanthomonas campestris (Xcc1752)
ComponentsCellulase
KeywordsHYDROLASE / Glycoside Hydrolase Family 74 / Xyloglucanase / Xyloglucan
Function / homology: / xyloglucan metabolic process / hydrolase activity, acting on glycosyl bonds / polysaccharide catabolic process / WD40/YVTN repeat-like-containing domain superfamily / IODIDE ION / Cellulase
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAraujo, E.A. / Vieira, P.S. / Murakami, M.T. / Polikarpov, I.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2016/06509-0 Brazil
Sao Paulo Research Foundation (FAPESP)2015/26982-0 Brazil
Sao Paulo Research Foundation (FAPESP)2015/13684-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)303988-2015-5 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 4, 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

Downloads & links

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Assembly

Deposited unit
A: Cellulase
B: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,94329
Polymers154,6132
Non-polymers3,33027
Water19,5281084
1
A: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,00315
Polymers77,3071
Non-polymers1,69614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellulase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,94114
Polymers77,3071
Non-polymers1,63413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.790, 100.430, 168.274
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Cellulase


Mass: 77306.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25) (bacteria)
Strain: ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25 / Gene: XCC1752 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q8P9U5
#2: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 474.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a212h-1a_1-5]/1-1-2/a4-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1109 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1084 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.23 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 mol/L sodium iodede 0.1 mol/L bis-tris propane 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: 1.45855 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 23, 2012
RadiationMonochromator: Water-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45855 Å / Relative weight: 1
ReflectionResolution: 1.95→19.992 Å / Num. obs: 99662 / % possible obs: 98.1 % / Redundancy: 12.191 % / CC1/2: 0.997 / Net I/σ(I): 11.02
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 10.12 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 15178 / CC1/2: 0.888 / % possible all: 93.7

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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: 2CN2

2cn2


Resolution: 1.95→19.992 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2515 5044 5.07 %
Rwork0.2163 94491 -
obs0.2181 99535 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.54 Å2 / Biso mean: 19.4244 Å2 / Biso min: 14.26 Å2
Refinement stepCycle: final / Resolution: 1.95→19.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10844 0 116 1084 12044
Biso mean--24.29 20.28 -
Num. residues----1415
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-1.97170.38111420.3211248979
1.9717-1.99480.32731590.2868308997
1.9948-2.01910.29451800.2859308298
2.0191-2.04470.32311720.2808307097
2.0447-2.07160.31221620.307308598
2.0716-2.09990.3461630.2732312597
2.0999-2.12990.31661590.2696314998
2.1299-2.16160.29921900.2559307597
2.1616-2.19540.29141660.2628311098
2.1954-2.23130.34641640.2787313298
2.2313-2.26970.35161700.3337307997
2.2697-2.31090.33091720.2766315399
2.3109-2.35530.27291600.2687312598
2.3553-2.40330.34521850.2456313498
2.4033-2.45550.2741420.249317299
2.4555-2.51250.29171570.2609315499
2.5125-2.57520.30271670.2255316298
2.5752-2.64470.23361830.2215316599
2.6447-2.72230.28941690.2243317799
2.7223-2.810.25761640.2134320099
2.81-2.91010.28341680.2072318499
2.9101-3.02620.26311590.2004320399
3.0262-3.16350.25061770.19623201100
3.1635-3.32950.20821500.18993227100
3.3295-3.53710.20741680.17913242100
3.5371-3.80840.18551770.16793235100
3.8084-4.18850.20861620.16883268100
4.1885-4.78730.15871760.1543272100
4.7873-6.00430.20191990.17933279100
6.0043-19.9920.20811820.20513453100

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