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

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Basic information

Entry
Database: PDB / ID: 7qhv
TitleCrystal structure of the sulfoquinovosyl binding protein SmoF complexed with sulfoquinovosyl diacylglycerol
ComponentsSulfoquinovosyl binding protein
KeywordsSUGAR BINDING PROTEIN / agrobacterium / sulfoquinovose / SmoF
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / Chem-CQI / GLYCINE / Maltose-binding periplasmic protein
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsSnow, A. / 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
DepositionDec 14, 2021Deposition 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

Downloads & links

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Assembly

Deposited unit
AAA: Sulfoquinovosyl binding protein
BBB: Sulfoquinovosyl binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5635
Polymers88,1502
Non-polymers1,4133
Water3,747208
1
AAA: Sulfoquinovosyl binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8193
Polymers44,0751
Non-polymers7442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Sulfoquinovosyl binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7442
Polymers44,0751
Non-polymers6691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.215, 69.589, 104.574
Angle α, β, γ (deg.)90.000, 91.539, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 44074.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: SY94_3278 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A083ZKV5
#2: Chemical ChemComp-CQI / [(2~{S},3~{S},4~{S},5~{R},6~{S})-6-[(2~{S})-3-butanoyloxy-2-heptanoyloxy-propoxy]-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid / sulfoquinovosyl diacylglycerol


Mass: 668.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H60O12S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M L-Na-glutamate, alanine, glycine, lysine hydrochloride, serine, 0.1M TRIS, bicine, 12.5% MPD, PEG1000, PEG3350

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Data collection

DiffractionMean temperature: 210 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97933 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.14→69.59 Å / Num. obs: 42301 / % possible obs: 99.9 % / Redundancy: 4.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.081 / Rrim(I) all: 0.124 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.08-69.593.80.0635900.9830.0550.084
2.14-2.24.10.30534620.9420.2650.406

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292119394

Resolution: 2.14→57.995 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.881 / SU ML: 0.177 / Cross valid method: FREE R-VALUE / ESU R: 0.277 / ESU R Free: 0.221
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2598 2124 5.024 %
Rwork0.2035 40153 -
all0.206 --
obs-42277 99.865 %
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: 24.287 Å2
Baniso -1Baniso -2Baniso -3
1-3.124 Å2-0 Å23.128 Å2
2---0.769 Å2-0 Å2
3----2.52 Å2
Refinement stepCycle: LAST / Resolution: 2.14→57.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5828 0 73 208 6109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136031
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175576
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.6438214
X-RAY DIFFRACTIONr_angle_other_deg1.31.57912825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39224.19253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80115929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6881517
X-RAY DIFFRACTIONr_chiral_restr0.0690.2817
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021307
X-RAY DIFFRACTIONr_nbd_refined0.2010.21337
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.25328
X-RAY DIFFRACTIONr_nbtor_refined0.1650.22975
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22703
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0430.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1110.23
X-RAY DIFFRACTIONr_nbd_other0.1730.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.211
X-RAY DIFFRACTIONr_mcbond_it1.6762.6013103
X-RAY DIFFRACTIONr_mcbond_other1.6772.63101
X-RAY DIFFRACTIONr_mcangle_it2.5533.8913870
X-RAY DIFFRACTIONr_mcangle_other2.5533.893870
X-RAY DIFFRACTIONr_scbond_it1.8872.6952928
X-RAY DIFFRACTIONr_scbond_other1.8852.6952928
X-RAY DIFFRACTIONr_scangle_it2.8843.9794344
X-RAY DIFFRACTIONr_scangle_other2.8833.9794344
X-RAY DIFFRACTIONr_lrange_it4.22230.7116865
X-RAY DIFFRACTIONr_lrange_other4.20430.6646843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.1950.2961600.252939X-RAY DIFFRACTION99.8389
2.195-2.2560.3031390.2522900X-RAY DIFFRACTION99.9671
2.256-2.3210.3211500.2342819X-RAY DIFFRACTION100
2.321-2.3920.2711420.2132679X-RAY DIFFRACTION99.9292
2.392-2.4710.2661550.2132625X-RAY DIFFRACTION99.964
2.471-2.5570.271410.2082551X-RAY DIFFRACTION99.9258
2.557-2.6540.2771350.2082482X-RAY DIFFRACTION99.8474
2.654-2.7620.2711240.2112354X-RAY DIFFRACTION99.9194
2.762-2.8850.261350.2052248X-RAY DIFFRACTION100
2.885-3.0260.2781100.2062205X-RAY DIFFRACTION100
3.026-3.1890.251050.1952066X-RAY DIFFRACTION100
3.189-3.3820.25860.1981984X-RAY DIFFRACTION99.663
3.382-3.6160.2591060.1931852X-RAY DIFFRACTION99.949
3.616-3.9050.253880.1841709X-RAY DIFFRACTION99.8888
3.905-4.2770.222840.1691592X-RAY DIFFRACTION99.9404
4.277-4.7810.191910.1581434X-RAY DIFFRACTION99.7384
4.781-5.5190.243590.1881280X-RAY DIFFRACTION99.7765
5.519-6.7540.345410.2381105X-RAY DIFFRACTION99.8258
6.754-9.5320.225490.196844X-RAY DIFFRACTION100
9.532-57.9950.275240.246485X-RAY DIFFRACTION98.835

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