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- PDB-5no8: Polysaccharide Lyase BACCELL_00875 -

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Basic information

Entry
Database: PDB / ID: 5no8
TitlePolysaccharide Lyase BACCELL_00875
ComponentsBACCELL_00875
KeywordsLYASE / Polysaccharide Lyase / Arabinogalactan / L-Rhamnose / Glucuronic Acid
Function / homologySix-hairpin glycosidase superfamily / carbohydrate metabolic process / Six-hairpin glycosidase
Function and homology information
Biological speciesBacteroides cellulosilyticus DSM 14838 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
CitationJournal: 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.
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 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BACCELL_00875
B: BACCELL_00875
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,92613
Polymers159,9132
Non-polymers1,01311
Water18,3571019
1
A: BACCELL_00875
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5097
Polymers79,9561
Non-polymers5536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BACCELL_00875
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4176
Polymers79,9561
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.542, 117.542, 201.984
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein BACCELL_00875


Mass: 79956.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides cellulosilyticus DSM 14838 (bacteria)
Gene: BACCELL_00875 / Production host: Escherichia coli (E. coli) / References: UniProt: E2N9D0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1019 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG1500, 0.1 M MMT buffer, pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→45.45 Å / Num. obs: 177287 / % possible obs: 100 % / Redundancy: 8.4 % / Net I/σ(I): 10.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.45 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.925 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18118 8840 5 %RANDOM
Rwork0.15842 ---
obs0.15958 168379 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å2-0 Å2
2---0.09 Å20 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.7→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10793 0 66 1019 11878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911267
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210034
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.94715287
X-RAY DIFFRACTIONr_angle_other_deg0.957323246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46751369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75423.91578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77151829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3271576
X-RAY DIFFRACTIONr_chiral_restr0.0910.21600
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212751
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022477
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_it1.2541.9345434
X-RAY DIFFRACTIONr_mcbond_other1.2531.9335433
X-RAY DIFFRACTIONr_mcangle_it1.8882.8936817
X-RAY DIFFRACTIONr_mcangle_other1.8882.8946818
X-RAY DIFFRACTIONr_scbond_it2.0142.1875833
X-RAY DIFFRACTIONr_scbond_other2.0142.1875833
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1913.1838471
X-RAY DIFFRACTIONr_long_range_B_refined4.67723.50313118
X-RAY DIFFRACTIONr_long_range_B_other4.67723.50413119
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 661 -
Rwork0.262 12295 -
obs--99.99 %

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