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- PDB-8qc5: crystal structure of NAD-dependent glycoside hydrolase from Arthr... -

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Basic information

Entry
Database: PDB / ID: 8qc5
Titlecrystal structure of NAD-dependent glycoside hydrolase from Arthrobacter sp. U41 in complex with NAD+ cofactor and citrate
ComponentsOxidoreductase
KeywordsHYDROLASE / NAD(H)-dependent / glycoside 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
CITRIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase
Similarity search - Component
Biological speciesArthrobacter sp. U41 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)87,5906
Polymers85,8792
Non-polymers1,7114
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALLS shows enzyme exists as dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-32 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.863, 72.817, 197.307
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 / 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: isolated from a natural source / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: protein was incubated with 2m M NAD+. crystals were grown in wells containing 1.8 M triammonium citrate pH7

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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: 1.95→49.33 Å / Num. obs: 60807 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.048 / Rrim(I) all: 0.18 / Χ2: 0.99 / Net I/σ(I): 11.9 / Num. measured all: 832666
Reflection shellResolution: 1.95→2 Å / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 1.251 / Num. measured all: 59824 / Num. unique obs: 4220 / CC1/2: 0.911 / Rpim(I) all: 0.343 / Rrim(I) all: 1.298 / Χ2: 0.97 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→49.3 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.148 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23857 3029 5 %RANDOM
Rwork0.19805 ---
obs0.2001 57694 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.385 Å2
Baniso -1Baniso -2Baniso -3
1-6.34 Å2-0 Å20 Å2
2---3.99 Å2-0 Å2
3----2.35 Å2
Refinement stepCycle: 1 / Resolution: 1.95→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5533 0 114 245 5892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125777
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165337
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.6557879
X-RAY DIFFRACTIONr_angle_other_deg0.4551.5712286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8135726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.251537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36710884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026749
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021241
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_it2.343.0362910
X-RAY DIFFRACTIONr_mcbond_other2.3393.0372910
X-RAY DIFFRACTIONr_mcangle_it3.2585.4463634
X-RAY DIFFRACTIONr_mcangle_other3.2585.4473635
X-RAY DIFFRACTIONr_scbond_it3.2273.2242867
X-RAY DIFFRACTIONr_scbond_other3.2243.2212864
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.555.8244246
X-RAY DIFFRACTIONr_long_range_B_refined6.06436.6424467
X-RAY DIFFRACTIONr_long_range_B_other6.06436.6424468
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 211 -
Rwork0.296 4206 -
obs--100 %

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