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- PDB-8qc2: Crystal structure of NAD-dependent glycoside hydrolase from Flavo... -

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Basic information

Entry
Database: PDB / ID: 8qc2
TitleCrystal structure of NAD-dependent glycoside hydrolase from Flavobacterium sp. (strain K172) in complex with co-factor NAD+ and sulfoquinovose (SQ)
ComponentsGfo/Idh/MocA family oxidoreductase
KeywordsHYDROLASE / oxidoreductive / sulfoquinovose / glycoside hydrolase
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / sulfoquinovose / :
Function and homology information
Biological speciesPaenarthrobacter ureafaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPickles, I.B. / Sharma, M. / Davies, G.J.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)951231European Union
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: Gfo/Idh/MocA family oxidoreductase
B: Gfo/Idh/MocA family oxidoreductase
C: Gfo/Idh/MocA family oxidoreductase
D: Gfo/Idh/MocA family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,88918
Polymers171,5254
Non-polymers4,36314
Water13,331740
1
A: Gfo/Idh/MocA family oxidoreductase
C: Gfo/Idh/MocA family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9449
Polymers85,7632
Non-polymers2,1827
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-28 kcal/mol
Surface area25840 Å2
MethodPISA
2
B: Gfo/Idh/MocA family oxidoreductase
D: Gfo/Idh/MocA family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9449
Polymers85,7632
Non-polymers2,1827
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-30 kcal/mol
Surface area25820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.517, 160.381, 185.749
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-675-

HOH

21A-700-

HOH

31B-624-

HOH

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Components

#1: Protein
Gfo/Idh/MocA family oxidoreductase


Mass: 42881.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter ureafaciens (bacteria)
Gene: FV140_09610 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7D7VZ79
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: isolated from a natural source / 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.: 4 / Source method: obtained synthetically / Formula: C6H12O8S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / 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: 2.42 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM bis-tris propane pH 7, 0.02 mM sodium and potassium phosphate, 28% (w/v) PEG3350, 5 mM NAD+ and 1 mM manganese chloride. SQ powder soaked into the well directly for around 2 minutes

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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 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→51.19 Å / Num. obs: 73391 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.288 / Rpim(I) all: 0.08 / Rrim(I) all: 0.299 / Χ2: 0.88 / Net I/σ(I): 6.2 / Num. measured all: 1014728
Reflection shellResolution: 2.3→2.35 Å / % possible obs: 100 % / Redundancy: 14.4 % / Rmerge(I) obs: 1.616 / Num. measured all: 64373 / Num. unique obs: 4478 / CC1/2: 0.876 / Rpim(I) all: 0.438 / Rrim(I) all: 1.675 / Χ2: 0.85 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.06 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.836 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24593 3609 4.9 %RANDOM
Rwork0.19499 ---
obs0.19748 69673 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.867 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0 Å2
2---3.47 Å2-0 Å2
3---3.55 Å2
Refinement stepCycle: 1 / Resolution: 2.3→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11072 0 284 740 12096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01211606
X-RAY DIFFRACTIONr_bond_other_d0.0020.01610686
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.66215833
X-RAY DIFFRACTIONr_angle_other_deg0.4841.57524623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02351448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.194572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.504101771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.21827
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213472
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022468
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_it2.8753.0785810
X-RAY DIFFRACTIONr_mcbond_other2.8743.0775804
X-RAY DIFFRACTIONr_mcangle_it4.2985.5247248
X-RAY DIFFRACTIONr_mcangle_other4.2985.5247249
X-RAY DIFFRACTIONr_scbond_it3.8323.375796
X-RAY DIFFRACTIONr_scbond_other3.8313.375797
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9666.0338586
X-RAY DIFFRACTIONr_long_range_B_refined7.13829.0512611
X-RAY DIFFRACTIONr_long_range_B_other7.13829.0512612
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 283 -
Rwork0.316 5093 -
obs--99.81 %

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