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- PDB-8tcr: Structure of glucose bound Alistipes sp. 3-Keto-beta-glucopyranos... -

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Basic information

Entry
Database: PDB / ID: 8tcr
TitleStructure of glucose bound Alistipes sp. 3-Keto-beta-glucopyranoside-1,2-Lyase AL1
ComponentsSugar phosphate isomerase
KeywordsISOMERASE / Sugar Phosphate Isomerase
Function / homology: / alpha-D-glucopyranose / MALONATE ION / :
Function and homology information
Biological speciesAlistipes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 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
C: Sugar phosphate isomerase
B: Sugar phosphate isomerase
A: Sugar phosphate isomerase
D: Sugar phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,09219
Polymers130,9534
Non-polymers2,13915
Water5,639313
1
C: Sugar phosphate isomerase
B: Sugar phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,59710
Polymers65,4762
Non-polymers1,1218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sugar phosphate isomerase
D: Sugar phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4959
Polymers65,4762
Non-polymers1,0197
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.517, 113.679, 208.580
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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 1500 0.13 M MIB 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: 2.08→47.4 Å / Num. obs: 68867 / % possible obs: 99.8 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.06 / Rrim(I) all: 0.085 / Χ2: 0.94 / Net I/σ(I): 8.9 / Num. measured all: 130468
Reflection shellResolution: 2.08→2.13 Å / % possible obs: 98.2 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.53 / Num. measured all: 8537 / Num. unique obs: 4460 / CC1/2: 0.566 / Rpim(I) all: 0.53 / Rrim(I) all: 0.749 / Χ2: 0.93 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→47.4 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.563 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22898 3475 5 %RANDOM
Rwork0.18192 ---
obs0.18429 65376 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.288 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å2-0 Å2
2--1.13 Å2-0 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 2.08→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8622 0 131 313 9066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0128956
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168227
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.83712083
X-RAY DIFFRACTIONr_angle_other_deg0.5871.76919081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54451076
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.262529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.022101553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.21286
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210229
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021971
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_it2.3523.1474316
X-RAY DIFFRACTIONr_mcbond_other2.353.1474316
X-RAY DIFFRACTIONr_mcangle_it3.2875.6475388
X-RAY DIFFRACTIONr_mcangle_other3.2875.6475389
X-RAY DIFFRACTIONr_scbond_it3.2623.5124640
X-RAY DIFFRACTIONr_scbond_other3.2623.5124641
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.996.2856696
X-RAY DIFFRACTIONr_long_range_B_refined7.25139.5239948
X-RAY DIFFRACTIONr_long_range_B_other7.25139.5239949
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 247 -
Rwork0.302 4634 -
obs--97.91 %

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