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- PDB-7yzs: Crystal structure of the sulfoquinovosyl binding protein SmoF com... -

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Basic information

Entry
Database: PDB / ID: 7yzs
TitleCrystal structure of the sulfoquinovosyl binding protein SmoF complexed with sulfoquinovose
ComponentsSulfoquinovosyl binding protein
KeywordsSUGAR BINDING PROTEIN / agrobacterium / sulfoquinovose / SmoF
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / 6-deoxy-6-sulfo-beta-D-glucopyranose / Maltose-binding periplasmic protein
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSnow, A.J.D. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2017-190 United Kingdom
CitationJournal: Curr Res Struct Biol / Year: 2022
Title: The sulfoquinovosyl glycerol binding protein SmoF binds and accommodates plant sulfolipids.
Authors: Snow, A.J.D. / Sharma, M. / Lingford, J.P. / Zhang, Y. / Mui, J.W. / Epa, R. / Goddard-Borger, E.D. / Williams, S.J. / Davies, G.J.
History
DepositionFeb 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Sulfoquinovosyl binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3192
Polymers44,0751
Non-polymers2441
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.198, 102.198, 67.959
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Sulfoquinovosyl binding protein / Maltose-binding periplasmic protein


Mass: 44074.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: SY94_3278 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A083ZKV5
#2: Sugar ChemComp-YZT / 6-deoxy-6-sulfo-beta-D-glucopyranose


Type: saccharide / Mass: 244.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.1 M NaBr, NaI, 0.1 M imidazole, MES pH 6.9, 13.5% MPD, PEG 1000, PEG 3350

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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 PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→88.51 Å / Num. obs: 38278 / % possible obs: 100 % / Redundancy: 19.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.179 / Net I/σ(I): 10.1
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 2247 / CC1/2: 0.654

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OFY

6ofy


Resolution: 1.8→88.51 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.234 --
Rwork0.198 --
obs-38250 100 %
Refinement stepCycle: LAST / Resolution: 1.8→88.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 15 137 3053

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