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- PDB-8tcd: Structure of Alistipes sp. 3-Keto-beta-glucopyranoside-1,2-Lyase AL1 -

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Basic information

Entry
Database: PDB / ID: 8tcd
TitleStructure of Alistipes sp. 3-Keto-beta-glucopyranoside-1,2-Lyase AL1
ComponentsSugar phosphate isomerase
KeywordsISOMERASE / Sugar Phosphate Isomerase
Function / homologyACETATE ION / : / :
Function and homology information
Biological speciesAlistipes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionJun 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 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

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Assembly

Deposited unit
B: Sugar phosphate isomerase
C: Sugar phosphate isomerase
D: Sugar phosphate isomerase
A: Sugar phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,67514
Polymers130,9534
Non-polymers72210
Water9,278515
1
B: Sugar phosphate isomerase
C: Sugar phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8387
Polymers65,4762
Non-polymers3615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Sugar phosphate isomerase
A: Sugar phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8387
Polymers65,4762
Non-polymers3615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.574, 112.608, 209.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Sugar phosphate isomerase


Mass: 32738.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alistipes (bacteria) / Gene: A5CPYCFAH4_05830 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y1X717
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.27 M Ammonium Chloride 17% 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: CLSI / Beamline: 08B1-1 / Wavelength: 1.1808 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 1.9→47.57 Å / Num. obs: 89795 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.07 / Rrim(I) all: 0.177 / Χ2: 1.03 / Net I/σ(I): 9.7 / Num. measured all: 577872
Reflection shellResolution: 1.9→1.93 Å / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 1.954 / Num. measured all: 26884 / Num. unique obs: 4511 / CC1/2: 0.507 / Rpim(I) all: 0.876 / Rrim(I) all: 2.145 / Χ2: 1.24 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.39 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.257 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22836 4533 5.1 %RANDOM
Rwork0.19065 ---
obs0.19258 85162 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.987 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.9→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8635 0 36 515 9186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0128868
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168185
X-RAY DIFFRACTIONr_angle_refined_deg1.611.83311950
X-RAY DIFFRACTIONr_angle_other_deg0.5441.76918954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65351081
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.113529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.451101549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.21245
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021968
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_it1.9922.2974338
X-RAY DIFFRACTIONr_mcbond_other1.9832.2974337
X-RAY DIFFRACTIONr_mcangle_it3.0084.1195413
X-RAY DIFFRACTIONr_mcangle_other3.0084.125414
X-RAY DIFFRACTIONr_scbond_it2.5322.5244530
X-RAY DIFFRACTIONr_scbond_other2.5322.5244531
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0114.5046538
X-RAY DIFFRACTIONr_long_range_B_refined5.99428.1839855
X-RAY DIFFRACTIONr_long_range_B_other5.99428.1839856
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 309 -
Rwork0.349 6186 -
obs--99.78 %

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