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- PDB-5nok: Polysaccharide Lyase BACCELL_00875 -

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Basic information

Entry
Database: PDB / ID: 5nok
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 / SAD / Resolution: 2.24 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 12, 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 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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)161,6093
Polymers161,4142
Non-polymers1951
Water4,396244
1
A: BACCELL_00875


Theoretical massNumber of molelcules
Total (without water)80,7071
Polymers80,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BACCELL_00875
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9022
Polymers80,7071
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.730, 116.730, 228.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein BACCELL_00875


Mass: 80706.773 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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.46 %
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: I02 / 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: 2.24→47.48 Å / Num. obs: 76640 / % possible obs: 100 % / Redundancy: 43.2 % / Rmerge(I) obs: 0.0131 / Net I/σ(I): 10.6
Reflection shellResolution: 2.24→2.29 Å / Rmerge(I) obs: 0.3201

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
XDSdata reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.24→47.48 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.078 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24925 3842 5 %RANDOM
Rwork0.19499 ---
obs0.19768 72698 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.015 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å2-0 Å2-0 Å2
2--1.09 Å2-0 Å2
3----2.18 Å2
Refinement stepCycle: 1 / Resolution: 2.24→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10688 0 12 244 10944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910971
X-RAY DIFFRACTIONr_bond_other_d0.0020.029700
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.95114892
X-RAY DIFFRACTIONr_angle_other_deg0.978322418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77151334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57423.872563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.217151652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2511574
X-RAY DIFFRACTIONr_chiral_restr0.0870.21562
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212433
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022425
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_it2.2853.9775345
X-RAY DIFFRACTIONr_mcbond_other2.2843.9775344
X-RAY DIFFRACTIONr_mcangle_it3.475.9596676
X-RAY DIFFRACTIONr_mcangle_other3.475.9596677
X-RAY DIFFRACTIONr_scbond_it2.8514.2445626
X-RAY DIFFRACTIONr_scbond_other2.8514.2445626
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5676.2448217
X-RAY DIFFRACTIONr_long_range_B_refined6.02146.10512158
X-RAY DIFFRACTIONr_long_range_B_other6.02146.09812157
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 295 -
Rwork0.289 5268 -
obs--99.98 %

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