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- PDB-6xn2: Crystal structure of the GH43_1 enzyme from Xanthomonas citri com... -

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Basic information

Entry
Database: PDB / ID: 6xn2
TitleCrystal structure of the GH43_1 enzyme from Xanthomonas citri complexed with xylotriose
ComponentsXylosidase
KeywordsHYDROLASE / glycoside hydrolase / GH43
Function / homologyGlycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / 4beta-beta-xylotriose / DI(HYDROXYETHYL)ETHER / beta-D-xylopyranose / Xylosidase
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.652 Å
AuthorsMorais, M.A.B. / Tonoli, C.C.C. / Santos, C.R. / Murakami, M.T.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/26982-0 Brazil
Sao Paulo Research Foundation (FAPESP)2016/19995-0 Brazil
CitationJournal: Nat Commun / Year: 2021
Title: Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations.
Authors: Morais, M.A.B. / Coines, J. / Domingues, M.N. / Pirolla, R.A.S. / Tonoli, C.C.C. / Santos, C.R. / Correa, J.B.L. / Gozzo, F.C. / Rovira, C. / Murakami, M.T.
History
DepositionJul 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _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: Xylosidase
B: Xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,23517
Polymers80,4512
Non-polymers1,78415
Water9,044502
1
A: Xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0389
Polymers40,2261
Non-polymers8138
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1978
Polymers40,2261
Non-polymers9717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.593, 165.874, 158.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Xylosidase


Mass: 40225.578 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: xsa, XAC4258 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PET2

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 414.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylotriose
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 515 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2 M ammonium sulfate, 30% (w/v) Polietilenoglicol 8,000, 0.1 M sodium cacodylate pH 6.5 and 10 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.65→29.413 Å / Num. obs: 63992 / % possible obs: 63.6 % / Redundancy: 4.343 % / Biso Wilson estimate: 30.13 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.057 / Χ2: 0.948 / Net I/σ(I): 16.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.752.1080.5051.23112551608353380.7450.62133.2
1.75-1.872.5190.2832.5177631515970510.9160.3446.5
1.87-2.023.1830.1645.43243841410876610.970.19254.3
2.02-2.224.1040.1139.05333531303781270.9890.12862.3
2.22-2.484.5170.09612.83377061180883480.9920.10870.7
2.48-2.864.9930.06418.59414531045983020.9960.07179.4
2.86-3.55.3740.04927.5343989889681850.9980.05492
3.5-4.936.1620.0438.4342648696969210.9980.04499.3
4.93-29.4136.2870.03542.1125005402039770.9980.03898.9

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Processing

Software
NameVersionClassification
PHENIX1.8refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MLG

4mlg


Resolution: 1.652→29.41 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2008 3166 4.95 %
Rwork0.1767 60800 -
obs0.1779 63966 63.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.38 Å2 / Biso mean: 34.45 Å2 / Biso min: 21.19 Å2
Refinement stepCycle: final / Resolution: 1.652→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5192 0 124 502 5818
Biso mean--48.42 36.97 -
Num. residues----661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0215493
X-RAY DIFFRACTIONf_angle_d1.4957485
X-RAY DIFFRACTIONf_chiral_restr0.114760
X-RAY DIFFRACTIONf_plane_restr0.009975
X-RAY DIFFRACTIONf_dihedral_angle_d14.791990
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6525-1.67710.4767640.4689123030
1.6771-1.70330.4492640.3448131532
1.7033-1.73120.3685700.3162141935
1.7312-1.76110.3207850.2876157438
1.7611-1.79310.3324910.275171642
1.7931-1.82760.29851080.281191547
1.8276-1.86490.25921040.2523213452
1.8649-1.90540.27331000.275216353
1.9054-1.94980.35791030.3191218453
1.9498-1.99850.24071210.2171229455
1.9985-2.05250.23241180.2073242859
2.0525-2.11290.23441350.2047252561
2.1129-2.18110.25771450.1951262064
2.1811-2.2590.28961490.2399269966
2.259-2.34940.22191520.2045288670
2.3494-2.45630.21261410.1957314175
2.4563-2.58570.22731770.1948318777
2.5857-2.74760.21251950.1974330380
2.7476-2.95960.19861830.1904342882
2.9596-3.25710.17842210.1775382892
3.2571-3.72760.19362090.161419799
3.7276-4.69330.1522000.1333424399
4.6933-29.410.18262310.1496437199

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