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- PDB-7erl: GH43 domain of bifunctional endoxylanase and arabinofuranosidase ... -

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Basic information

Entry
Database: PDB / ID: 7erl
TitleGH43 domain of bifunctional endoxylanase and arabinofuranosidase of Bi0569
ComponentsBeta-xylanaseXylanase
KeywordsHYDROLASE / endo-xylanase / arabinofuranosidase
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesBacteroides intestinalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.89329827548 Å
AuthorsLiu, D. / Wang, C.
CitationJournal: To Be Published
Title: Structure of bifunctional endoxylanase and arabinofuranosidaseat GH43 domain of Bi0569 protein
Authors: Liu, D. / Wang, C.
History
DepositionMay 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-xylanase
B: Beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5216
Polymers121,7412
Non-polymers7814
Water8,773487
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.790, 103.585, 167.768
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-xylanase / Xylanase


Mass: 60870.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides intestinalis (bacteria) / Gene: BILFYP9_04406 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6N2X8R5, endo-1,4-beta-xylanase
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: PEG3350 15% ,0.2M NH4CL,0.1M MES6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jan 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 102587 / % possible obs: 95 % / Redundancy: 1 % / Biso Wilson estimate: 25.4983130399 Å2 / CC1/2: 1 / Net I/σ(I): 35.72
Reflection shellResolution: 1.8→10 Å / Num. unique obs: 50 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
cctbx.xfeldata reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.89329827548→49.4879367867 Å / SU ML: 0.18635863549 / Cross valid method: FREE R-VALUE / σ(F): 1.36423523087 / Phase error: 18.7818848346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.202526614625 5182 5.05137153218 %
Rwork0.172262209269 97404 -
obs0.173777286973 102586 99.6503021001 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.0826909965 Å2
Refinement stepCycle: LAST / Resolution: 1.89329827548→49.4879367867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8546 0 48 487 9081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007594205676398838
X-RAY DIFFRACTIONf_angle_d0.97423232494512023
X-RAY DIFFRACTIONf_chiral_restr0.06507474772261259
X-RAY DIFFRACTIONf_plane_restr0.005743278006441586
X-RAY DIFFRACTIONf_dihedral_angle_d3.760836590375169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8933-1.91480.3048486181861450.2525358691932953X-RAY DIFFRACTION92.8378783338
1.9148-1.93730.2782568436481670.2383384349843233X-RAY DIFFRACTION99.9118424919
1.9373-1.9610.2823544455541560.2195367678013230X-RAY DIFFRACTION99.8820058997
1.961-1.98580.2790337109811860.2096705372763245X-RAY DIFFRACTION99.9417419167
1.9858-2.01190.2320135970561580.1996662442443179X-RAY DIFFRACTION99.8503889886
2.0119-2.03950.2403702658941690.2015573174183229X-RAY DIFFRACTION99.8237367803
2.0395-2.06860.217800372041750.2020174347223223X-RAY DIFFRACTION99.8824221046
2.0686-2.09950.2254078736621690.1933187066023215X-RAY DIFFRACTION99.8524638536
2.0995-2.13230.2423666665011770.1813057497853199X-RAY DIFFRACTION99.9703879183
2.1323-2.16730.2215286891241980.1725776786113230X-RAY DIFFRACTION99.8834498834
2.1673-2.20460.1879666007261820.1776931734883220X-RAY DIFFRACTION99.9118942731
2.2046-2.24470.2151171765591710.179872686173220X-RAY DIFFRACTION99.9705188679
2.2447-2.28790.2169248002381860.177915646563216X-RAY DIFFRACTION99.8825601879
2.2879-2.33460.2194863973851730.1736629184363213X-RAY DIFFRACTION99.9114783122
2.3346-2.38540.2109527650461720.1704165937423259X-RAY DIFFRACTION99.9708624709
2.3854-2.44080.1967868406841510.1720656476143261X-RAY DIFFRACTION99.8829039813
2.4408-2.50190.2030349564781780.1658299651423222X-RAY DIFFRACTION99.8238402819
2.5019-2.56950.2199360430641550.1668648954933264X-RAY DIFFRACTION99.9415375621
2.5695-2.64510.1948210720421800.1719207132353263X-RAY DIFFRACTION99.9419448476
2.6451-2.73050.2304439372581800.1690384293783244X-RAY DIFFRACTION99.9124598774
2.7305-2.82810.1852566347011490.1605056569163270X-RAY DIFFRACTION99.9707602339
2.8281-2.94130.2077139868211930.1586255174423241X-RAY DIFFRACTION99.9708879185
2.9413-3.07520.1873242869721930.1540013765733243X-RAY DIFFRACTION100
3.0752-3.23730.1682909687121810.1518480759233280X-RAY DIFFRACTION99.9711149624
3.2373-3.440.154377314551410.1470276376773299X-RAY DIFFRACTION100
3.44-3.70560.189768150741820.1515693444663290X-RAY DIFFRACTION100
3.7056-4.07830.177992107611870.1613657009173286X-RAY DIFFRACTION100
4.0783-4.66810.1887344236531750.1590208097993326X-RAY DIFFRACTION99.8289136014
4.6681-5.87970.2023265413921830.1831751890113349X-RAY DIFFRACTION99.8868778281
5.8797-100.212846611361700.2021814934533502X-RAY DIFFRACTION98.9757412399

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