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- PDB-8tdf: Structure of Alistipes sp. Glucoside-3-dehydrogenase AL3 -

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Basic information

Entry
Database: PDB / ID: 8tdf
TitleStructure of Alistipes sp. Glucoside-3-dehydrogenase AL3
ComponentsDehydrogenase
KeywordsISOMERASE / Oxidoreductase / Dehydrogenase
Function / homologyGfo/Idh/MocA-like oxidoreductase, bacterial type, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NAD(P)-binding domain superfamily / nucleotide binding / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dehydrogenase
Function and homology information
Biological speciesAlistipes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

Downloads & links

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Assembly

Deposited unit
A: Dehydrogenase
B: Dehydrogenase
C: Dehydrogenase
D: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,6978
Polymers210,0434
Non-polymers2,6544
Water7,458414
1
A: Dehydrogenase
B: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3484
Polymers105,0222
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-37 kcal/mol
Surface area34310 Å2
MethodPISA
2
C: Dehydrogenase
D: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3484
Polymers105,0222
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-31 kcal/mol
Surface area34120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.635, 56.751, 220.447
Angle α, β, γ (deg.)90.00, 108.87, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein
Dehydrogenase


Mass: 52510.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alistipes (bacteria) / Gene: A3BBH6_04580 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y1WH70
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15 M Sodium Malonate 19% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→48 Å / Num. obs: 123819 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.073 / Rrim(I) all: 0.189 / Χ2: 0.99 / Net I/σ(I): 7.2 / Num. measured all: 822967
Reflection shellResolution: 2.1→2.14 Å / % possible obs: 99.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.619 / Num. measured all: 41507 / Num. unique obs: 6021 / CC1/2: 0.513 / Rpim(I) all: 0.659 / Rrim(I) all: 1.75 / Χ2: 1.05 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 13.269 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23265 6343 5.1 %RANDOM
Rwork0.19848 ---
obs0.20027 117468 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.456 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å20 Å2-0.91 Å2
2--1.88 Å2-0 Å2
3----2.95 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14249 0 176 414 14839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01214837
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613735
X-RAY DIFFRACTIONr_angle_refined_deg2.0651.66320188
X-RAY DIFFRACTIONr_angle_other_deg0.6711.58831698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55651804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.65596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.571102395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.22132
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217548
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023404
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_it2.0831.5217228
X-RAY DIFFRACTIONr_mcbond_other2.081.5217228
X-RAY DIFFRACTIONr_mcangle_it3.2192.7189028
X-RAY DIFFRACTIONr_mcangle_other3.2192.7199029
X-RAY DIFFRACTIONr_scbond_it2.981.7987609
X-RAY DIFFRACTIONr_scbond_other2.9791.7987610
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5043.14511161
X-RAY DIFFRACTIONr_long_range_B_refined6.93515.2916739
X-RAY DIFFRACTIONr_long_range_B_other6.93315.2416679
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 442 -
Rwork0.297 8578 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.49070.0966-0.33140.7608-0.13431.8858-0.0325-0.02690.00610.0635-0.03280.05030.1195-0.20840.06530.0969-0.0137-0.01230.0344-0.0210.331523.141-2.23931.182
21.33990.1865-0.13170.8571-0.00681.1163-0.0837-0.2322-0.11920.0803-0.0219-0.21590.13230.7020.10560.14790.1051-0.01220.49020.07350.416364.853-6.2730.172
30.8906-0.15620.04850.8517-0.40631.8349-0.00320.26980.18020.0303-0.03090.0291-0.6504-0.21730.03410.5195-0.1056-0.07010.32530.04770.405825.143-27.861-22.965
41.1662-0.1145-0.07740.7127-0.17561.14150.07640.2717-0.0028-0.1187-0.15-0.2094-0.04020.37890.07360.4004-0.288-0.03740.60630.09330.495665.179-39.493-27.109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 490
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION2B39 - 490
4X-RAY DIFFRACTION2B501
5X-RAY DIFFRACTION3C39 - 490
6X-RAY DIFFRACTION3C501
7X-RAY DIFFRACTION4D39 - 490
8X-RAY DIFFRACTION4D501

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