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- PDB-8qc3: Crystal structure of oxidoreductive sulfoquinovosidase from Arthr... -

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Basic information

Entry
Database: PDB / ID: 8qc3
TitleCrystal structure of oxidoreductive sulfoquinovosidase from Arthrobacter sp. U41 (ArSqgA)in complex with co-factor NAD+
ComponentsOxidoreductase
KeywordsHYDROLASE / oxidoreductive / sulfoquinovose / glycoside hydrolase
Function / homology: / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily / nucleotide binding / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase
Function and homology information
Biological speciesArthrobacter sp. U41 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSharma, M. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W003805/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Widespread Family of NAD + -Dependent Sulfoquinovosidases at the Gateway to Sulfoquinovose Catabolism.
Authors: Kaur, A. / Pickles, I.B. / Sharma, M. / Madeido Soler, N. / Scott, N.E. / Pidot, S.J. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J.
History
DepositionAug 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2064
Polymers85,8792
Non-polymers1,3272
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Sec-MALLS shows enzyme forms dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-36 kcal/mol
Surface area25940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.273, 53.994, 90.721
Angle α, β, γ (deg.)90.00, 90.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Oxidoreductase


Mass: 42939.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. U41 (bacteria) / Gene: ASPU41_10185 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C9WRL0
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.2 M potassium nitrate pH 6.8, 20% (w/v) PEG3350, 2 mM NAD+

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.65→45.36 Å / Num. obs: 20601 / % possible obs: 98.7 % / Redundancy: 6.3 % / CC1/2: 0.961 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.072 / Rrim(I) all: 0.18 / Χ2: 0.88 / Net I/σ(I): 7 / Num. measured all: 130389
Reflection shellResolution: 2.65→2.78 Å / % possible obs: 98.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.785 / Num. measured all: 17890 / Num. unique obs: 2715 / CC1/2: 0.709 / Rpim(I) all: 0.336 / Rrim(I) all: 0.856 / Χ2: 0.93 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→45.3 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.872 / SU B: 17.762 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27482 1014 4.9 %RANDOM
Rwork0.21689 ---
obs0.21974 19552 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.535 Å2
Baniso -1Baniso -2Baniso -3
1--5.43 Å20 Å23.01 Å2
2--6.3 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 2.65→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5420 0 88 31 5539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125635
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165173
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.6547697
X-RAY DIFFRACTIONr_angle_other_deg0.4661.56911869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3415726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.12536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7910826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021220
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_it3.5314.2062910
X-RAY DIFFRACTIONr_mcbond_other3.5314.2062910
X-RAY DIFFRACTIONr_mcangle_it5.5537.563634
X-RAY DIFFRACTIONr_mcangle_other5.5527.563635
X-RAY DIFFRACTIONr_scbond_it3.4584.2612725
X-RAY DIFFRACTIONr_scbond_other3.4584.2612726
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5027.7654064
X-RAY DIFFRACTIONr_long_range_B_refined8.07837.815894
X-RAY DIFFRACTIONr_long_range_B_other8.07737.815895
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 82 -
Rwork0.341 1427 -
obs--97.73 %

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