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- PDB-8tcs: Structure of trehalose bound Alistipes sp. 3-Keto-beta-glucopyran... -

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Basic information

Entry
Database: PDB / ID: 8tcs
TitleStructure of trehalose bound Alistipes sp. 3-Keto-beta-glucopyranoside-1,2-Lyase AL1
ComponentsXylose isomerase-like TIM barrel domain-containing protein
KeywordsISOMERASE / Sugar Phosphate Isomerase
Function / homologyXylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / trehalose / ACETATE ION / : / Xylose isomerase-like TIM barrel domain-containing protein
Function and homology information
Biological speciesAlistipes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLazarski, A.C. / Worrall, L.J. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nature / Year: 2024
Title: An alternative broad-specificity pathway for glycan breakdown in bacteria.
Authors: Nasseri, S.A. / Lazarski, A.C. / Lemmer, I.L. / Zhang, C.Y. / Brencher, E. / Chen, H.M. / Sim, L. / Panwar, D. / Betschart, L. / Worrall, L.J. / Brumer, H. / Strynadka, N.C.J. / Withers, S.G.
History
DepositionJul 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
D: Xylose isomerase-like TIM barrel domain-containing protein
C: Xylose isomerase-like TIM barrel domain-containing protein
A: Xylose isomerase-like TIM barrel domain-containing protein
B: Xylose isomerase-like TIM barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,71213
Polymers123,0484
Non-polymers1,6649
Water15,619867
1
D: Xylose isomerase-like TIM barrel domain-containing protein
A: Xylose isomerase-like TIM barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3266
Polymers61,5242
Non-polymers8024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Xylose isomerase-like TIM barrel domain-containing protein
B: Xylose isomerase-like TIM barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3857
Polymers61,5242
Non-polymers8625
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.994, 113.549, 212.442
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Xylose isomerase-like TIM barrel domain-containing protein


Mass: 30761.924 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alistipes (bacteria) / Gene: BN590_01572 / Production host: Escherichia coli (E. coli) / References: UniProt: R6XSE3
#2: Polysaccharide
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 867 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.44 M Ammonium Chloride 21% PEG 6000 0.1 M Sodium Acetate pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.5→48.11 Å / Num. obs: 186241 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.043 / Rrim(I) all: 0.079 / Net I/σ(I): 11
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.327 / Num. unique obs: 18379 / CC1/2: 0.543 / Rpim(I) all: 0.844 / Rrim(I) all: 1.578

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→44.335 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.175 / SU B: 1.661 / SU ML: 0.059 / Average fsc free: 0.9608 / Average fsc work: 0.9691 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 9367 5.033 %RANDOM
Rwork0.1735 176754 --
all0.175 ---
obs-186121 99.826 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--1.249 Å20 Å2-0 Å2
2--0.672 Å2-0 Å2
3---0.577 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8610 0 100 867 9577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0129009
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168234
X-RAY DIFFRACTIONr_angle_refined_deg3.4411.83812163
X-RAY DIFFRACTIONr_angle_other_deg0.6441.76719097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46851095
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.241529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.253101556
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.94510424
X-RAY DIFFRACTIONr_chiral_restr0.0950.21290
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210356
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021996
X-RAY DIFFRACTIONr_nbd_refined0.2350.21719
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.27374
X-RAY DIFFRACTIONr_nbtor_refined0.1880.24358
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.24570
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2633
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.240.227
X-RAY DIFFRACTIONr_nbd_other0.1970.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2360.251
X-RAY DIFFRACTIONr_mcbond_it2.2642.4264357
X-RAY DIFFRACTIONr_mcbond_other2.2582.4264356
X-RAY DIFFRACTIONr_mcangle_it3.0984.3595447
X-RAY DIFFRACTIONr_mcangle_other3.0994.3595448
X-RAY DIFFRACTIONr_scbond_it3.9292.8234652
X-RAY DIFFRACTIONr_scbond_other3.9282.8234653
X-RAY DIFFRACTIONr_scangle_it5.4814.9956704
X-RAY DIFFRACTIONr_scangle_other5.484.9956705
X-RAY DIFFRACTIONr_lrange_it6.77630.03110365
X-RAY DIFFRACTIONr_lrange_other6.77630.0310366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.3156710.297129170.298135890.9210.92599.99260.295
1.539-1.5810.2936850.278126060.279133000.9290.93699.93230.273
1.581-1.6270.2816670.259122290.26129020.940.94799.95350.251
1.627-1.6770.2616700.234118810.236125580.9520.95999.94430.223
1.677-1.7320.2625860.224116280.226122150.9550.96699.99180.211
1.732-1.7920.2435760.2112120.203117960.9620.97499.93220.184
1.792-1.860.2265990.192108190.193114200.9670.97799.98250.174
1.86-1.9360.2225420.19104360.192109890.9680.97799.89990.173
1.936-2.0220.2255630.1899670.182105400.9690.9899.90510.163
2.022-2.120.2155120.17295650.174100810.9710.98199.96030.159
2.12-2.2350.2214610.16691680.16896360.970.98399.92740.154
2.235-2.370.1914460.16186690.16291220.9790.98499.92330.153
2.37-2.5330.1984070.1682010.16286210.9750.98499.84920.157
2.533-2.7350.2183960.16375540.16679730.970.98399.71150.164
2.735-2.9950.193630.16170570.16274460.9770.98499.65080.166
2.995-3.3460.1963330.16863390.1767070.9770.98399.47820.177
3.346-3.860.1712950.16256490.16259750.9840.98699.48120.176
3.86-4.7190.162620.13748170.13851340.9870.9998.92870.159
4.719-6.6360.1991940.16537910.16640280.9840.98898.93250.186
6.636-44.3350.2081390.17822490.17924040.980.98299.33440.216

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