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- PDB-6xn0: Crystal structure of GH43_1 enzyme from Xanthomonas citri -

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Basic information

Entry
Database: PDB / ID: 6xn0
TitleCrystal structure of GH43_1 enzyme from Xanthomonas citri
ComponentsXylosidase
KeywordsHYDROLASE / glycoside hydrolase / GH43 / exo-oligoxylanase
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 / DI(HYDROXYETHYL)ETHER / Xylosidase
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.709 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)82,45724
Polymers80,4512
Non-polymers2,00622
Water8,467470
1
A: Xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,30713
Polymers40,2261
Non-polymers1,08112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,15111
Polymers40,2261
Non-polymers92510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.557, 165.914, 158.709
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
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: 1.709→47.94 Å / Num. obs: 90908 / % possible obs: 98.5 % / Redundancy: 6.002 % / Biso Wilson estimate: 27.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.083 / Χ2: 1.026 / Net I/σ(I): 14.04
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
1.71-1.814.3960.9871.296129414756139430.7511.11994.5
1.81-1.945.5490.483.297600513895136960.9240.52998.6
1.94-2.096.5860.2716.568444812972128220.9730.29598.8
2.09-2.296.3570.16510.227547811933118730.9880.1899.5
2.29-2.566.470.11314.496997110854108140.9940.12399.6
2.56-2.966.5130.07521.1962392960195790.9970.08299.8
2.96-3.626.1880.05330.2650237816581190.9980.05899.4
3.62-5.16.6420.04240.0742401639363840.9980.04699.9
5.1-426.3750.03939.8623449370936780.9980.04399.2

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4mlg


Resolution: 1.709→42 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 4555 5.01 %
Rwork0.1714 86336 -
obs0.173 90891 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.74 Å2 / Biso mean: 30.81 Å2 / Biso min: 17.05 Å2
Refinement stepCycle: final / Resolution: 1.709→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5160 0 128 470 5758
Biso mean--47.19 38.66 -
Num. residues----656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135468
X-RAY DIFFRACTIONf_angle_d1.4587442
X-RAY DIFFRACTIONf_chiral_restr0.067756
X-RAY DIFFRACTIONf_plane_restr0.007972
X-RAY DIFFRACTIONf_dihedral_angle_d14.6251916
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7093-1.72870.54381140.4637237282
1.7287-1.74910.35231510.3611277596
1.7491-1.77040.30881440.3188285999
1.7704-1.79280.30391570.3012278197
1.7928-1.81640.35891650.3228287599
1.8164-1.84130.33711390.3033282597
1.8413-1.86760.30691430.2651286899
1.8676-1.89550.27661700.2314285798
1.8955-1.92510.30111420.208283899
1.9251-1.95660.23811500.1998287698
1.9566-1.99040.21631360.17832887100
1.9904-2.02660.21641570.1752286098
2.0266-2.06550.21741510.17712872100
2.0655-2.10770.20891680.1734285799
2.1077-2.15350.2181550.1755287199
2.1535-2.20360.21311500.1652897100
2.2036-2.25870.19491330.1609290099
2.2587-2.31980.22491510.1621291899
2.3198-2.38810.2111480.16172915100
2.3881-2.46510.21491520.16732901100
2.4651-2.55320.21421420.16692939100
2.5532-2.65540.19581680.16112889100
2.6554-2.77630.19661630.15872923100
2.7763-2.92260.17831640.1552903100
2.9226-3.10570.16851390.15572955100
3.1057-3.34540.16771700.1552291599
3.3454-3.68180.18451490.1467293699
3.6818-4.21420.18381640.14252971100
4.2142-5.30770.16731460.14633011100

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