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- PDB-6q64: BT1044SeMet E190Q -

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Basic information

Entry
Database: PDB / ID: 6q64
TitleBT1044SeMet E190Q
ComponentsEndoglycosidase
KeywordsHYDROLASE / Glycoside hydrolase family 18 / complex N-glycans
Function / homologyGlycoside hydrolase family 18, BT1044-like / Glycoside hydrolase family 18, BT1044-like / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / carbohydrate metabolic process / Endoglycosidase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsBasle, A. / Paterson, N. / Crouch, L. / Bolam, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M029018/1 United Kingdom
CitationJournal: Nat Microbiol / Year: 2019
Title: Complex N-glycan breakdown by gut Bacteroides involves an extensive enzymatic apparatus encoded by multiple co-regulated genetic loci.
Authors: Briliute, J. / Urbanowicz, P.A. / Luis, A.S. / Basle, A. / Paterson, N. / Rebello, O. / Hendel, J. / Ndeh, D.A. / Lowe, E.C. / Martens, E.C. / Spencer, D.I.R. / Bolam, D.N. / Crouch, L.I.
History
DepositionDec 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglycosidase


Theoretical massNumber of molelcules
Total (without water)42,1181
Polymers42,1181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.584, 119.584, 83.094
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 Endoglycosidase / Glycoside hydrolase


Mass: 42117.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BJP75_026240, BSIG_0571, Btheta7330_02659, ERS852430_00349, ERS852511_00641, HMPREF2534_00734
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0FQI4

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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: 4.11 Å3/Da / Density % sol: 70.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200 mM NaF, Bis-Tris propane pH 6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 2.4→48.5 Å / Num. obs: 27124 / % possible obs: 99.8 % / Redundancy: 11.1 % / CC1/2: 0.999 / Net I/σ(I): 12.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2797 / CC1/2: 0.835 / % possible all: 99.5

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Processing

Software
NameClassification
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
REFMACrefinement
Cootmodel building
RefinementResolution: 2.4→43.99 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 28.885 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24364 1318 4.9 %RANDOM
Rwork0.19712 ---
obs0.1993 25784 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.88 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å21.37 Å20 Å2
2--2.74 Å2-0 Å2
3----8.89 Å2
Refinement stepCycle: 1 / Resolution: 2.4→43.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 0 0 2633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132705
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172401
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.6543670
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5775598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1075325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.58123.655145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.88815430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9361511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023039
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02578
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_it3.5175.9531303
X-RAY DIFFRACTIONr_mcbond_other3.5195.9511302
X-RAY DIFFRACTIONr_mcangle_it5.1768.9361627
X-RAY DIFFRACTIONr_mcangle_other5.1748.9391628
X-RAY DIFFRACTIONr_scbond_it3.6236.3151402
X-RAY DIFFRACTIONr_scbond_other3.626.3091400
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.59.342043
X-RAY DIFFRACTIONr_long_range_B_refined7.54268.9723088
X-RAY DIFFRACTIONr_long_range_B_other7.54368.8993086
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 86 -
Rwork0.426 1883 -
obs--99.49 %
Refinement TLS params.Method: refined / Origin x: 46.0134 Å / Origin y: 50.4194 Å / Origin z: 23.5 Å
111213212223313233
T0.1817 Å20.1532 Å20.0143 Å2-0.2559 Å2-0.0448 Å2--0.1 Å2
L1.6114 °2-0.3133 °21.0686 °2-1.3309 °2-0.3485 °2--4.2027 °2
S-0.182 Å °-0.2504 Å °0.2635 Å °0.2322 Å °0.0312 Å °0.2172 Å °-0.4546 Å °-0.8204 Å °0.1508 Å °

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