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- PDB-8tdi: Structure of P2B11 Glucuronide-3-dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 8tdi
TitleStructure of P2B11 Glucuronide-3-dehydrogenase
ComponentsP2B11 Glucuronide-3-dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesCollinsella tanakaei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 3, 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_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: P2B11 Glucuronide-3-dehydrogenase
J: P2B11 Glucuronide-3-dehydrogenase
A: P2B11 Glucuronide-3-dehydrogenase
C: P2B11 Glucuronide-3-dehydrogenase
D: P2B11 Glucuronide-3-dehydrogenase
E: P2B11 Glucuronide-3-dehydrogenase
F: P2B11 Glucuronide-3-dehydrogenase
G: P2B11 Glucuronide-3-dehydrogenase
H: P2B11 Glucuronide-3-dehydrogenase
I: P2B11 Glucuronide-3-dehydrogenase
B: P2B11 Glucuronide-3-dehydrogenase
K: P2B11 Glucuronide-3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)553,85546
Polymers543,57212
Non-polymers10,28334
Water4,414245
1
L: P2B11 Glucuronide-3-dehydrogenase
J: P2B11 Glucuronide-3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2367
Polymers90,5952
Non-polymers1,6415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-42 kcal/mol
Surface area29020 Å2
MethodPISA
2
A: P2B11 Glucuronide-3-dehydrogenase
G: P2B11 Glucuronide-3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3598
Polymers90,5952
Non-polymers1,7636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-29 kcal/mol
Surface area29390 Å2
MethodPISA
3
C: P2B11 Glucuronide-3-dehydrogenase
K: P2B11 Glucuronide-3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2107
Polymers90,5952
Non-polymers1,6155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-42 kcal/mol
Surface area28040 Å2
MethodPISA
4
D: P2B11 Glucuronide-3-dehydrogenase
B: P2B11 Glucuronide-3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3598
Polymers90,5952
Non-polymers1,7636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-28 kcal/mol
Surface area29070 Å2
MethodPISA
5
E: P2B11 Glucuronide-3-dehydrogenase
H: P2B11 Glucuronide-3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3338
Polymers90,5952
Non-polymers1,7376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-36 kcal/mol
Surface area29040 Å2
MethodPISA
6
F: P2B11 Glucuronide-3-dehydrogenase
I: P2B11 Glucuronide-3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3598
Polymers90,5952
Non-polymers1,7636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-26 kcal/mol
Surface area29310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.260, 185.878, 145.362
Angle α, β, γ (deg.)90.00, 111.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
P2B11 Glucuronide-3-dehydrogenase


Mass: 45297.680 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Collinsella tanakaei (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M LiSO4 19% 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: 1.18 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.6→48.37 Å / Num. obs: 161121 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.049 / Rrim(I) all: 0.13 / Χ2: 1.02 / Net I/σ(I): 13.7 / Num. measured all: 1108051
Reflection shellResolution: 2.6→2.64 Å / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 1.919 / Num. measured all: 55713 / Num. unique obs: 7990 / CC1/2: 0.373 / Rpim(I) all: 0.78 / Rrim(I) all: 2.074 / Χ2: 1.02 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→48.37 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 16.924 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R: 1.404 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25694 8026 5 %RANDOM
Rwork0.21574 ---
obs0.2178 153057 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.856 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å2-0 Å20.9 Å2
2---1.5 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 2.6→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35839 0 662 245 36746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01237376
X-RAY DIFFRACTIONr_bond_other_d0.0010.01633795
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.81550862
X-RAY DIFFRACTIONr_angle_other_deg0.5261.76277917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67354539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.765204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.244105905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.25468
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0244286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028498
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_it6.6367.13218260
X-RAY DIFFRACTIONr_mcbond_other6.6357.13218260
X-RAY DIFFRACTIONr_mcangle_it9.77212.78622759
X-RAY DIFFRACTIONr_mcangle_other9.77212.78622760
X-RAY DIFFRACTIONr_scbond_it6.6567.46919116
X-RAY DIFFRACTIONr_scbond_other6.6277.4519061
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.94613.52628020
X-RAY DIFFRACTIONr_long_range_B_refined14.62586.63163805
X-RAY DIFFRACTIONr_long_range_B_other14.62786.65163732
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 557 -
Rwork0.361 11265 -
obs--99.96 %

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