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- PDB-8bvk: The crystal structure of O-glycoside cleaving beta-eliminase from... -

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Basic information

Entry
Database: PDB / ID: 8bvk
TitleThe crystal structure of O-glycoside cleaving beta-eliminase from A. tumefaciens AtOGE
ComponentsXylose isomerase
KeywordsHYDROLASE / O-glycoside cleaving beta-eliminase / A. tumefaciens / AtOGE
Function / homologyXylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / isomerase activity / : / Xylose isomerase
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKuhlmann, K. / Bitter, J. / Pfeiffer, M. / Nidetzky, B. / Pavkov-Keller, T.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundDOC130 Austria
CitationJournal: Nat Commun / Year: 2023
Title: Enzymatic beta-elimination in natural product O- and C-glycoside deglycosylation.
Authors: Bitter, J. / Pfeiffer, M. / Borg, A.J.E. / Kuhlmann, K. / Pavkov-Keller, T. / Sanchez-Murcia, P.A. / Nidetzky, B.
History
DepositionDec 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylose isomerase
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9785
Polymers55,8132
Non-polymers1653
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PDBePISA suggests a dimer with a single significant contact site (surface area 19380 sq. Angstroem)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-26 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.580, 93.670, 123.680
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 Xylose isomerase


Mass: 27906.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: BV900_26275 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V2ADZ4
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
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: 1.9 Å3/Da / Density % sol: 35.2 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium chloridenitrate, containing 20% (w/v) PEG 3350; 10 mg/mL AtOGE1 in buffer C (10 mM HEPES buffer pH 7.0 containing 150 mM NaCl and 0.1 mM TCEP) and 0.04 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.995→46.84 Å / Num. obs: 55224 / % possible obs: 99.03 % / Redundancy: 12.5 % / Biso Wilson estimate: 28.81 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0794 / Rpim(I) all: 0.0234 / Rrim(I) all: 0.0829 / Net I/σ(I): 20.3
Reflection shellResolution: 1.995→2.067 Å / Redundancy: 12 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 6.24 / Num. unique obs: 2699 / CC1/2: 0.985 / CC star: 0.996 / Rpim(I) all: 0.0859 / Rrim(I) all: 0.3038 / % possible all: 91.99

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIXv1.16-3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.84 Å / SU ML: 0.2233 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.1849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2175 2090 3.78 %
Rwork0.1742 53134 -
obs0.1758 55224 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.22 Å2
Refinement stepCycle: LAST / Resolution: 2→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 3 302 3644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613405
X-RAY DIFFRACTIONf_angle_d0.78734619
X-RAY DIFFRACTIONf_chiral_restr0.05530
X-RAY DIFFRACTIONf_plane_restr0.0053596
X-RAY DIFFRACTIONf_dihedral_angle_d3.08952045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.281180.2213130X-RAY DIFFRACTION86.18
2.04-2.090.29441340.17883567X-RAY DIFFRACTION99.87
2.09-2.150.26571400.17583603X-RAY DIFFRACTION99.97
2.15-2.210.22951400.17883513X-RAY DIFFRACTION99.89
2.21-2.280.24161500.18053652X-RAY DIFFRACTION99.89
2.28-2.370.21751390.18253483X-RAY DIFFRACTION99.72
2.37-2.460.23611420.19043589X-RAY DIFFRACTION99.39
2.46-2.570.26511430.18843588X-RAY DIFFRACTION99.92
2.57-2.710.24761450.18523570X-RAY DIFFRACTION100
2.71-2.880.22731430.18733575X-RAY DIFFRACTION99.89
2.88-3.10.23191350.19693568X-RAY DIFFRACTION99.84
3.1-3.410.22771380.18933589X-RAY DIFFRACTION99.63
3.41-3.90.19771420.16213557X-RAY DIFFRACTION99.2
3.9-4.920.15731400.14713557X-RAY DIFFRACTION99.73
4.92-46.840.21181410.16233593X-RAY DIFFRACTION99.73

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