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- PDB-5noa: Polysaccharide Lyase BACCELL_00875 -

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Basic information

Entry
Database: PDB / ID: 5noa
TitlePolysaccharide Lyase BACCELL_00875
ComponentsFamily 88 glycosyl hydrolase
KeywordsHYDROLASE / Human Gut Microbiota / Polysaccharide lyase / Bacteroides thetaiotaomicron / Gum Arabic
Function / homology
Function and homology information


unsaturated rhamnogalacturonyl hydrolase / unsaturated rhamnogalacturonyl hydrolase activity / hydrolase activity / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolase, family 88 / Glycosyl Hydrolase Family 88 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Glycoside hydrolase family 88 protein / Glycosyl hydrolase, family 88
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsCartmell, A. / Munoz-Munoz, J. / Terrapon, N. / Basle, A. / Henrissat, B. / Gilbert, H.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council322820 United Kingdom
Citation
Journal: J. Biol. Chem. / Year: 2017
Title: An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins.
Authors: Munoz-Munoz, J. / Cartmell, A. / Terrapon, N. / Basle, A. / Henrissat, B. / Gilbert, H.J.
#1: Journal: To Be Published
Title: Rhamnose Capping in Complex Arabinogalactan Proteins
Authors: Munoz-Munoz, J. / Cartmell, A. / Terrapon, N. / Basle, A. / Henrissat, B.
History
DepositionApr 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jan 17, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Family 88 glycosyl hydrolase


Theoretical massNumber of molelcules
Total (without water)43,6731
Polymers43,6731
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.398, 88.398, 215.857
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

21A-451-

HOH

31A-667-

HOH

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Components

#1: Protein Family 88 glycosyl hydrolase / Unsaturated rhamnogalacturonyl hydrolase YteR


Mass: 43673.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: yteR_9, BJP75_03260, Btheta7330_04609 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0P0FFM3, UniProt: Q8A1H4*PLUS, unsaturated rhamnogalacturonyl hydrolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

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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: 1.86 Å3/Da / Density % sol: 33.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium malonate 20% polyethylene glycol (PEG) 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.26→21.13 Å / Num. obs: 87238 / % possible obs: 99.5 % / Redundancy: 8.8 % / CC1/2: 0.998 / Net I/σ(I): 13
Reflection shellResolution: 1.26→1.28 Å / Redundancy: 3.9 % / Num. unique obs: 4048 / CC1/2: 0.524 / % possible all: 94.3

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimlessdata scaling
MrBUMPphasing
PHASERphasing
BUCCANEERmodel building
ARPmodel building
WARPmodel building
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CE7

4ce7


Resolution: 1.26→21.13 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.167 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14801 4229 4.9 %RANDOM
Rwork0.12135 ---
obs0.12268 81513 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.271 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.26→21.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 0 0 299 3192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193011
X-RAY DIFFRACTIONr_bond_other_d0.0020.022606
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9234097
X-RAY DIFFRACTIONr_angle_other_deg0.99436057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7435359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73724.038156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53515475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8411513
X-RAY DIFFRACTIONr_chiral_restr0.1130.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023403
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02674
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1660.9971421
X-RAY DIFFRACTIONr_mcbond_other1.1490.9951420
X-RAY DIFFRACTIONr_mcangle_it1.5351.5051776
X-RAY DIFFRACTIONr_mcangle_other1.5391.5071777
X-RAY DIFFRACTIONr_scbond_it1.8641.2851590
X-RAY DIFFRACTIONr_scbond_other1.8631.2841590
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2381.8312318
X-RAY DIFFRACTIONr_long_range_B_refined2.45412.763732
X-RAY DIFFRACTIONr_long_range_B_other2.34912.4553684
X-RAY DIFFRACTIONr_rigid_bond_restr1.95435617
X-RAY DIFFRACTIONr_sphericity_free18.4435207
X-RAY DIFFRACTIONr_sphericity_bonded6.21555612
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 253 -
Rwork0.242 5447 -
obs--88.88 %

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