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- PDB-6xn1: Crystal structure of the GH43_1 enzyme from Xanthomonas citri com... -

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Basic information

Entry
Database: PDB / ID: 6xn1
TitleCrystal structure of the GH43_1 enzyme from Xanthomonas citri complexed with xylose
ComponentsXylosidase
KeywordsHYDROLASE / glycoside hydrolase / GH43 / xylose
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 / beta-D-xylopyranose / Xylosidase
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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)81,65214
Polymers80,4512
Non-polymers1,20112
Water12,106672
1
A: Xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9188
Polymers40,2261
Non-polymers6937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7346
Polymers40,2261
Non-polymers5095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.431, 165.682, 159.109
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 / Sugars , 2 types, 4 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
#3: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
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, 682 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
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: 1.8→48.33 Å / Num. obs: 77797 / % possible obs: 97.1 % / Redundancy: 4.966 % / Biso Wilson estimate: 24.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.062 / Χ2: 0.933 / Net I/σ(I): 16.74
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
1.8-1.912.8780.5891.873284012818114120.8040.71789
1.91-2.043.5060.2514.444054412039115650.9510.29696.1
2.04-2.214.4040.1587.934809611209109210.9820.1897.4
2.21-2.425.3650.11112.235546210360103380.9940.12399.8
2.42-2.76.3890.0916.9859950939593840.9970.09899.9
2.7-3.126.1780.05825.351258831382970.9980.06399.8
3.12-3.816.1670.03936.7243543708170610.9990.04399.7
3.81-5.386.1990.03543.5934286555855310.9990.03999.5
5.38-36.7396.2230.03545.4419859322131910.9990.03899.1

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4mlg


Resolution: 1.8→36.739 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 3839 4.94 %
Rwork0.1729 73945 -
obs0.1746 77784 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.14 Å2 / Biso mean: 25.98 Å2 / Biso min: 13.34 Å2
Refinement stepCycle: final / Resolution: 1.8→36.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5197 0 76 672 5945
Biso mean--37.34 31.58 -
Num. residues----662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015441
X-RAY DIFFRACTIONf_angle_d1.2447424
X-RAY DIFFRACTIONf_chiral_restr0.054760
X-RAY DIFFRACTIONf_plane_restr0.007973
X-RAY DIFFRACTIONf_dihedral_angle_d13.8151930
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.803-1.82540.45361010.3963242285
1.8254-1.84940.31751450.3047246590
1.8494-1.87470.28951370.2729250990
1.8747-1.90150.32061170.2641254491
1.9015-1.92990.27091310.249260093
1.9299-1.960.27971360.2308262595
1.96-1.99220.25131470.2136269296
1.9922-2.02650.24021330.2033275898
2.0265-2.06340.24351160.2071278999
2.0634-2.10310.23631340.2032274198
2.1031-2.1460.25471280.2085264394
2.146-2.19260.23191460.1948276199
2.1926-2.24360.25031420.1792799100
2.2436-2.29970.21661510.17252800100
2.2997-2.36190.21121350.17222815100
2.3619-2.43140.25941300.1752822100
2.4314-2.50980.22761610.17772778100
2.5098-2.59950.23621410.17562805100
2.5995-2.70360.25191580.17542811100
2.7036-2.82660.2031400.172803100
2.8266-2.97550.20471550.17842836100
2.9755-3.16190.20951450.17222792100
3.1619-3.40580.20951710.17422807100
3.4058-3.74830.19921450.15332847100
3.7483-4.290.16851610.13672845100
4.29-5.40210.13561650.1174286199

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