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

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Basic information

Entry
Database: PDB / ID: 7yzu
TitleCrystal structure of the sulfoquinovosyl binding protein SmoF complexed with SQMe
ComponentsSulfoquinovosyl binding protein
KeywordsSUGAR BINDING PROTEIN / agrobacterium / sulfoquinovose / SmoF
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / Chem-DO7 / Maltose-binding periplasmic protein
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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 1.1May 1, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfoquinovosyl binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3332
Polymers44,0751
Non-polymers2581
Water5,386299
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)66.270, 99.380, 53.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: Chemical ChemComp-DO7 / [(2S,3S,4S,5R,6S)-6-methoxy-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid / Methylsulfoquinovoside


Mass: 258.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.3 M sodium acetate, 0.1 M BIS-TRIS (pH 5.5) and 35% PEG 2000 MME

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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: Feb 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.59→47.33 Å / Num. obs: 48233 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 0.98 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.148 / Rrim(I) all: 0.302 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID
1.59-1.625.622700.6791
8.71-47.286.9482330.981

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 70FY

70fy


Resolution: 1.59→47.33 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.66 / SU ML: 0.119 / Cross valid method: FREE R-VALUE / ESU R: 0.121 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2669 2429 5.042 %
Rwork0.2377 45750 -
all0.239 --
obs-48179 99.234 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.698 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2--2.683 Å2-0 Å2
3----1.833 Å2
Refinement stepCycle: LAST / Resolution: 1.59→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 16 299 3230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132994
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162805
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.6414073
X-RAY DIFFRACTIONr_angle_other_deg1.3831.5826469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4225380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25924.375128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22715488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.047158
X-RAY DIFFRACTIONr_chiral_restr0.0760.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023377
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02647
X-RAY DIFFRACTIONr_nbd_refined0.2140.2670
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.22637
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21497
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21345
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2230
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.10.28
X-RAY DIFFRACTIONr_nbd_other0.190.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.214
X-RAY DIFFRACTIONr_mcbond_it1.2651.8861526
X-RAY DIFFRACTIONr_mcbond_other1.2641.8851525
X-RAY DIFFRACTIONr_mcangle_it1.8532.8251904
X-RAY DIFFRACTIONr_mcangle_other1.8532.8261905
X-RAY DIFFRACTIONr_scbond_it1.7842.0291468
X-RAY DIFFRACTIONr_scbond_other1.7842.0281469
X-RAY DIFFRACTIONr_scangle_it2.6112.972169
X-RAY DIFFRACTIONr_scangle_other2.6112.972170
X-RAY DIFFRACTIONr_lrange_it3.91923.1743532
X-RAY DIFFRACTIONr_lrange_other3.79622.9113481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.6310.3321870.3583216X-RAY DIFFRACTION96.1028
1.631-1.6750.3491650.3333240X-RAY DIFFRACTION98.2401
1.675-1.7240.3111630.3063135X-RAY DIFFRACTION98.8017
1.724-1.7770.311550.2873080X-RAY DIFFRACTION98.839
1.777-1.8350.31610.2672984X-RAY DIFFRACTION99.3367
1.835-1.90.2871520.2772909X-RAY DIFFRACTION99.7718
1.9-1.9710.2921530.2452774X-RAY DIFFRACTION99.8295
1.971-2.0520.3181560.242710X-RAY DIFFRACTION99.9303
2.052-2.1430.2731260.2222639X-RAY DIFFRACTION100
2.143-2.2480.3171360.2332488X-RAY DIFFRACTION99.8858
2.248-2.3690.271400.2242357X-RAY DIFFRACTION99.92
2.369-2.5130.2621050.2232270X-RAY DIFFRACTION99.9159
2.513-2.6860.2791210.2182118X-RAY DIFFRACTION99.9108
2.686-2.9010.2811030.2291982X-RAY DIFFRACTION99.9042
2.901-3.1780.2591010.2311836X-RAY DIFFRACTION99.8454
3.178-3.5520.228820.2231677X-RAY DIFFRACTION100
3.552-4.1010.189740.2041482X-RAY DIFFRACTION99.4249
4.101-5.0210.248630.2081266X-RAY DIFFRACTION99.0313
5.021-7.0910.217540.251997X-RAY DIFFRACTION99.8101
7.091-47.330.232320.226590X-RAY DIFFRACTION97.9528

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