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- PDB-8qc6: Crystal Structure of NAD-dependent glycoside hydrolase from Arthr... -

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Basic information

Entry
Database: PDB / ID: 8qc6
TitleCrystal Structure of NAD-dependent glycoside hydrolase from Arthrobacter sp. U41 in complex with NAD+ and sulfoquinovose (SQ)
ComponentsOxidoreductase
KeywordsHYDROLASE / NAD(H)-dependent / glysoside hydrolase / sulfoquinovose / sulfoglycolysis
Function / homology
Function and homology information


: / 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
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / sulfoquinovose / Oxidoreductase
Similarity search - Component
Biological speciesArthrobacter sp. U41 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6946
Polymers85,8792
Non-polymers1,8154
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, exists as dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-40 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.561, 73.017, 199.502
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 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 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: Chemical ChemComp-R7R / sulfoquinovose / [(2~{S},3~{S},4~{S},5~{R},6~{S})-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methanesulfonic acid


Mass: 244.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O8S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4→58.92 Å / Num. obs: 33269 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.989 / Rmerge(I) obs: 0.277 / Rpim(I) all: 0.079 / Rrim(I) all: 0.288 / Χ2: 0.93 / Net I/σ(I): 6.6 / Num. measured all: 437041
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 99.7 % / Redundancy: 11.9 % / Rmerge(I) obs: 1.15 / Num. measured all: 40866 / Num. unique obs: 3423 / CC1/2: 0.723 / Rpim(I) all: 0.338 / Rrim(I) all: 1.201 / Χ2: 0.93 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→58.81 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.994 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24385 1655 5 %RANDOM
Rwork0.18561 ---
obs0.18848 31535 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.341 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å2-0 Å20 Å2
2---1.91 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 2.4→58.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 118 195 5883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125824
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165373
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.6617946
X-RAY DIFFRACTIONr_angle_other_deg0.4461.57212379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7095731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.229539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93310894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026787
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021255
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_it2.5172.9212924
X-RAY DIFFRACTIONr_mcbond_other2.5172.9212924
X-RAY DIFFRACTIONr_mcangle_it3.8025.2443652
X-RAY DIFFRACTIONr_mcangle_other3.8025.2453653
X-RAY DIFFRACTIONr_scbond_it2.9193.0832900
X-RAY DIFFRACTIONr_scbond_other2.9183.0832901
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3955.5774294
X-RAY DIFFRACTIONr_long_range_B_refined6.51434.8424286
X-RAY DIFFRACTIONr_long_range_B_other6.51434.8424286
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 114 -
Rwork0.277 2291 -
obs--99.42 %

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