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- PDB-8v31: Structure of Alistipes sp. 3-Keto-2-hydroxy-glucal-hydratase AL2 -

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Basic information

Entry
Database: PDB / ID: 8v31
TitleStructure of Alistipes sp. 3-Keto-2-hydroxy-glucal-hydratase AL2
ComponentsGlycosyl hydrolase
KeywordsHYDROLASE / Hydratase / GH16-like
Function / homology3-keto-disaccharide hydrolase / 3-keto-alpha-glucoside-1,2-lyase-like domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / hydrolase activity / Glycosyl hydrolase
Function and homology information
Biological speciesAlistipes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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
DepositionNov 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl hydrolase
C: Glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9684
Polymers61,9192
Non-polymers492
Water72140
1
A: Glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9842
Polymers30,9591
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9842
Polymers30,9591
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.088, 95.088, 159.542
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Glycosyl hydrolase / 3-Keto-2-hydroxy-glucal-hydratase AL2


Mass: 30959.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alistipes (bacteria) / Gene: A3BBH6_04590 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y1WGD9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.36 Å3/Da / Density % sol: 63.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Magnesium Chloride, 25% PEG 3350, 0.1 M Bis-Tris methane pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18085 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18085 Å / Relative weight: 1
ReflectionResolution: 2.65→47.54 Å / Num. obs: 24911 / % possible obs: 99.9 % / Redundancy: 18.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.047 / Rrim(I) all: 0.15 / Net I/σ(I): 22.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.79-47.5416.80.0242491110.0080.025
2.65-2.7818.52.05732360.8680.7042.176

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→47.54 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 11.308 / SU ML: 0.225 / Cross valid method: FREE R-VALUE / ESU R: 0.387 / ESU R Free: 0.272
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2441 1229 4.982 %
Rwork0.1966 23441 -
all0.199 --
obs-24670 99.12 %
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: 61.222 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.39 Å20 Å2
2--0.78 Å20 Å2
3----2.53 Å2
Refinement stepCycle: LAST / Resolution: 2.65→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 2 40 3980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124051
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163643
X-RAY DIFFRACTIONr_angle_refined_deg2.6541.8085494
X-RAY DIFFRACTIONr_angle_other_deg0.8781.7788410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8915491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.262512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.30110645
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.75410210
X-RAY DIFFRACTIONr_chiral_restr0.1160.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024879
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02973
X-RAY DIFFRACTIONr_nbd_refined0.2120.2646
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2240.23253
X-RAY DIFFRACTIONr_nbtor_refined0.1980.21936
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.10.22187
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.286
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2750.22
X-RAY DIFFRACTIONr_nbd_other0.1730.223
X-RAY DIFFRACTIONr_mcbond_it8.5525.8841973
X-RAY DIFFRACTIONr_mcbond_other8.5035.8851973
X-RAY DIFFRACTIONr_mcangle_it10.36710.5672461
X-RAY DIFFRACTIONr_mcangle_other10.36510.5712462
X-RAY DIFFRACTIONr_scbond_it10.5316.3152078
X-RAY DIFFRACTIONr_scbond_other10.4976.3132077
X-RAY DIFFRACTIONr_scangle_it13.2211.3253033
X-RAY DIFFRACTIONr_scangle_other13.21711.3273034
X-RAY DIFFRACTIONr_lrange_it13.93754.034307
X-RAY DIFFRACTIONr_lrange_other13.94354.0554305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.7190.481910.4391663X-RAY DIFFRACTION97.7159
2.719-2.7930.337820.2891692X-RAY DIFFRACTION100
2.793-2.8740.325940.2451606X-RAY DIFFRACTION100
2.874-2.9620.337790.2241581X-RAY DIFFRACTION100
2.962-3.0580.294820.2071557X-RAY DIFFRACTION100
3.058-3.1650.252660.2011491X-RAY DIFFRACTION100
3.165-3.2840.241690.1911426X-RAY DIFFRACTION100
3.284-3.4180.264720.2141396X-RAY DIFFRACTION99.5929
3.418-3.5690.329630.2771299X-RAY DIFFRACTION97.4946
3.569-3.7420.316750.2791205X-RAY DIFFRACTION95.6652
3.742-3.9430.306750.2671170X-RAY DIFFRACTION95.5487
3.943-4.180.178570.1751129X-RAY DIFFRACTION98.751
4.18-4.4670.21520.131093X-RAY DIFFRACTION100
4.467-4.8210.141610.1171024X-RAY DIFFRACTION100
4.821-5.2760.182470.119948X-RAY DIFFRACTION100
5.276-5.8890.172380.131874X-RAY DIFFRACTION100
5.889-6.7830.157390.147767X-RAY DIFFRACTION100
6.783-8.2660.221420.169653X-RAY DIFFRACTION100
8.266-11.5170.238330.153529X-RAY DIFFRACTION100
11.517-47.540.243120.233338X-RAY DIFFRACTION100

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