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- PDB-6pal: Bacteroides uniformis endo-laminarinase BuGH158 from the beta(1,3... -

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Basic information

Entry
Database: PDB / ID: 6pal
TitleBacteroides uniformis endo-laminarinase BuGH158 from the beta(1,3)-glucan utilization locus
ComponentsUncharacterized protein
KeywordsHYDROLASE / laminarinase / endo-glucanase
Function / homologyGlycosyl hydrolases family 2, TIM barrel domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / ACETATE ION / Glycoside hydrolase family 2 TIM barrel-domain containing protein
Function and homology information
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.818 Å
AuthorsTamura, K. / Brumer, H. / van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Mbio / Year: 2020
Title: Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human GutBacteroides.
Authors: Dejean, G. / Tamura, K. / Cabrera, A. / Jain, N. / Pudlo, N.A. / Pereira, G. / Viborg, A.H. / Van Petegem, F. / Martens, E.C. / Brumer, H.
History
DepositionJun 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Data collection / Database references / Category: citation / citation_author / diffrn_detector
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_detector.pdbx_collection_date
Revision 1.2Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8477
Polymers91,5152
Non-polymers3325
Water11,800655
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-38 kcal/mol
Surface area31540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.675, 106.030, 126.977
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 45757.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Gene: Bun01g_20700, DWW83_06800 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A412SRH5
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 49.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1 M bicine pH 9.0 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.818→40.726 Å / Num. obs: 80471 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.032 / Rrim(I) all: 0.117 / Net I/σ(I): 14.8
Reflection shellResolution: 1.818→1.849 Å / Rmerge(I) obs: 1.479 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3966 / CC1/2: 0.69 / Rpim(I) all: 0.49 / Rrim(I) all: 1.56

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.818→40.726 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2058 4004 4.976 %
Rwork0.1693 --
all0.171 --
obs-80470 99.986 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.169 Å2
Baniso -1Baniso -2Baniso -3
1-1.353 Å20 Å20 Å2
2---0.588 Å20 Å2
3----0.765 Å2
Refinement stepCycle: LAST / Resolution: 1.818→40.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6302 0 21 655 6978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136537
X-RAY DIFFRACTIONr_bond_other_d0.0360.0175979
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.6428878
X-RAY DIFFRACTIONr_angle_other_deg2.3351.57513838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3515816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56522.716335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.281151095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5761538
X-RAY DIFFRACTIONr_chiral_restr0.0720.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027398
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021408
X-RAY DIFFRACTIONr_nbd_refined0.1990.21083
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.25531
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23188
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.22688
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2478
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0090.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.290.213
X-RAY DIFFRACTIONr_nbd_other0.2390.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2790.214
X-RAY DIFFRACTIONr_mcbond_it2.2082.6763256
X-RAY DIFFRACTIONr_mcbond_other2.2062.6763254
X-RAY DIFFRACTIONr_mcangle_it3.1023.9944072
X-RAY DIFFRACTIONr_mcangle_other3.1023.9954073
X-RAY DIFFRACTIONr_scbond_it3.0842.9913281
X-RAY DIFFRACTIONr_scbond_other3.082.9893278
X-RAY DIFFRACTIONr_scangle_it4.7344.3444806
X-RAY DIFFRACTIONr_scangle_other4.734.3414801
X-RAY DIFFRACTIONr_lrange_it6.04631.1917414
X-RAY DIFFRACTIONr_lrange_other5.95630.8387305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.818-1.8650.2792920.2625576X-RAY DIFFRACTION100
1.865-1.9160.2732570.2265480X-RAY DIFFRACTION100
1.916-1.9710.2352750.2055296X-RAY DIFFRACTION100
1.971-2.0320.2252830.1845114X-RAY DIFFRACTION100
2.032-2.0990.2122510.1715031X-RAY DIFFRACTION100
2.099-2.1720.2042480.1594857X-RAY DIFFRACTION100
2.172-2.2540.2172560.1594660X-RAY DIFFRACTION100
2.254-2.3460.212490.1494510X-RAY DIFFRACTION100
2.346-2.450.22330.1534290X-RAY DIFFRACTION100
2.45-2.570.2132270.1634129X-RAY DIFFRACTION100
2.57-2.7090.2261990.1653972X-RAY DIFFRACTION100
2.709-2.8730.2241870.1713744X-RAY DIFFRACTION100
2.873-3.0710.2361870.1863503X-RAY DIFFRACTION100
3.071-3.3170.2131650.183324X-RAY DIFFRACTION100
3.317-3.6320.1881680.1673035X-RAY DIFFRACTION100
3.632-4.060.1711480.1452755X-RAY DIFFRACTION100
4.06-4.6860.1631350.1322455X-RAY DIFFRACTION100
4.686-5.7350.191070.172105X-RAY DIFFRACTION100
5.735-8.090.217880.1991655X-RAY DIFFRACTION100
8.09-40.7260.203490.177976X-RAY DIFFRACTION98.9382

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