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- PDB-7nbz: Crystal structure of ligand free open conformation of sulfoquinov... -

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Basic information

Entry
Database: PDB / ID: 7nbz
TitleCrystal structure of ligand free open conformation of sulfoquinovosyl binding protein (SQBP) from Agrobacterium tumefaciens
ComponentsSulfoquinovosyl binding protein
KeywordsSUGAR BINDING PROTEIN / apo / binding protein / sulfoquinovose
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / ACETATE ION / Maltose-binding periplasmic protein
Function and homology information
Biological speciesRhizobium radiobacter (Agrobacterium genomosp. 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSnow, A. / Sharma, M. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2017-190 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria.
Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / ...Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / Ascher, D.B. / McConville, M.J. / Davies, G.J. / Williams, S.J. / Goddard-Borger, E.D.
History
DepositionJan 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Derived calculations / Category: atom_type / chem_comp_atom / chem_comp_bond / 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
B: Sulfoquinovosyl binding protein
C: Sulfoquinovosyl binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,4026
Polymers132,2253
Non-polymers1773
Water26,3741464
1
A: Sulfoquinovosyl binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1342
Polymers44,0751
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfoquinovosyl binding protein


Theoretical massNumber of molelcules
Total (without water)44,0751
Polymers44,0751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sulfoquinovosyl binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1933
Polymers44,0751
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.321, 78.212, 83.456
Angle α, β, γ (deg.)109.039, 106.865, 104.766
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 44074.840 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (Agrobacterium genomosp. 4)
Gene: SY94_3278 / Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A083ZKV5
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1464 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2275825 Å3/Da / Density % sol: 44.81749 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.3 M Ammonium Acetate 0.1 M Bis-TRIS pH 5.5 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→72.014 Å / Num. obs: 234884 / % possible obs: 93.3 % / Redundancy: 2.1 % / CC1/2: 0.995 / Net I/σ(I): 11.1
Reflection shellResolution: 1.35→1.37 Å / Num. unique obs: 8434 / CC1/2: 0.906

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
DIALSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292108223

Resolution: 1.35→72.014 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.186 / Average fsc free: 0.9747 / Average fsc work: 0.9812 / Cross valid method: FREE R-VALUE / ESU R: 0.013 / ESU R Free: 0.014
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2095 11842 5.042 %
Rwork0.1832 223041 -
all0.184 --
obs-234883 93.253 %
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: 14.291 Å2
Baniso -1Baniso -2Baniso -3
1-5.979 Å2-2.035 Å21.372 Å2
2---2.484 Å2-0.188 Å2
3----3.494 Å2
Refinement stepCycle: LAST / Resolution: 1.35→72.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8804 0 12 1464 10280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0139219
X-RAY DIFFRACTIONr_bond_other_d0.0360.0178659
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.63912553
X-RAY DIFFRACTIONr_angle_other_deg2.3731.58119966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62551192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84724.1400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.352151520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9571530
X-RAY DIFFRACTIONr_chiral_restr0.0990.21216
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210585
X-RAY DIFFRACTIONr_gen_planes_other0.0160.022026
X-RAY DIFFRACTIONr_nbd_refined0.2250.21880
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.27644
X-RAY DIFFRACTIONr_nbtor_refined0.1780.24568
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.23953
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2876
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3290.219
X-RAY DIFFRACTIONr_nbd_other0.3370.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.259
X-RAY DIFFRACTIONr_mcbond_it1.321.3314723
X-RAY DIFFRACTIONr_mcbond_other1.3121.334719
X-RAY DIFFRACTIONr_mcangle_it1.8731.995925
X-RAY DIFFRACTIONr_mcangle_other1.8741.9915926
X-RAY DIFFRACTIONr_scbond_it2.1561.4924496
X-RAY DIFFRACTIONr_scbond_other2.1561.4924497
X-RAY DIFFRACTIONr_scangle_it3.1222.1616627
X-RAY DIFFRACTIONr_scangle_other3.1222.1616628
X-RAY DIFFRACTIONr_lrange_it4.14917.11410914
X-RAY DIFFRACTIONr_lrange_other4.14917.11610915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3850.3836880.35312933X-RAY DIFFRACTION72.9801
1.385-1.4230.3238340.3115346X-RAY DIFFRACTION89.0234
1.423-1.4640.2758160.27515209X-RAY DIFFRACTION90.7212
1.464-1.5090.2558160.2314996X-RAY DIFFRACTION92.0212
1.509-1.5590.2368170.20814665X-RAY DIFFRACTION93.4339
1.559-1.6130.2417290.19714486X-RAY DIFFRACTION94.6795
1.613-1.6740.2276990.18613984X-RAY DIFFRACTION94.546
1.674-1.7430.2216610.17813619X-RAY DIFFRACTION95.2889
1.743-1.820.2117140.17512984X-RAY DIFFRACTION95.8438
1.82-1.9090.2076760.17412396X-RAY DIFFRACTION95.5765
1.909-2.0120.2196650.17811868X-RAY DIFFRACTION96.5562
2.012-2.1340.1986090.17511301X-RAY DIFFRACTION96.578
2.134-2.2810.1855410.16710614X-RAY DIFFRACTION96.6554
2.281-2.4640.1845210.1629965X-RAY DIFFRACTION97.2998
2.464-2.6990.1994920.1679207X-RAY DIFFRACTION97.6934
2.699-3.0170.1974160.178333X-RAY DIFFRACTION97.6887
3.017-3.4820.2063760.1757398X-RAY DIFFRACTION98.6924
3.482-4.2620.1693700.166201X-RAY DIFFRACTION98.5453
4.262-6.0170.1792290.1634900X-RAY DIFFRACTION99.0728
6.017-72.0140.2281730.2012636X-RAY DIFFRACTION99.293

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