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- PDB-7ofy: Crystal structure of SQ binding protein from Agrobacterium tumefa... -

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Basic information

Entry
Database: PDB / ID: 7ofy
TitleCrystal structure of SQ binding protein from Agrobacterium tumefaciens in complex with sulfoquinovosyl glycerol (SQGro)
ComponentsSulfoquinovosyl binding protein
KeywordsSUGAR BINDING PROTEIN / sulfoquinovosyl diglyceride / SQDG / sulfoquinovose glycerol / SQGro / sulfoglycolysis
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / Chem-VCW / Maltose-binding periplasmic protein
Function and homology information
Biological speciesRhizobium radiobacter (Agrobacterium genomosp. 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsJarva, M.A. / Sharma, M. / Goddard-Borger, E.D. / 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
DepositionMay 5, 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 1.2Jan 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
A: Sulfoquinovosyl binding protein
B: Sulfoquinovosyl binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,40714
Polymers88,1502
Non-polymers1,25712
Water10,305572
1
A: Sulfoquinovosyl binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7037
Polymers44,0751
Non-polymers6296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfoquinovosyl binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7037
Polymers44,0751
Non-polymers6296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.795, 137.802, 54.068
Angle α, β, γ (deg.)90.000, 118.710, 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.) Rhizobium radiobacter (Agrobacterium genomosp. 4)
Gene: SY94_3278 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A083ZKV5
#2: Chemical ChemComp-VCW / [(2S,3S,4S,5R,6S)-6-[(2R)-2,3-bis(oxidanyl)propoxy]-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid / sulfoquinovosyl glycerol / SQGro


Mass: 318.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18O10S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 1.99 Å3/Da / Density % sol: 38.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 32% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris chloride, pH9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953664 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953664 Å / Relative weight: 1
ReflectionResolution: 1.7→47.19 Å / Num. obs: 74322 / % possible obs: 98.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.048 / Rrim(I) all: 0.09 / Net I/σ(I): 9.8 / Num. measured all: 254947 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.730.8431331939120.5610.53211.496.8
9-47.190.0217435180.9990.0120.02335.998

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.9 Å45.61 Å
Translation1.9 Å45.61 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.1phasing
PHENIX1.13refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DTQ

6dtq


Resolution: 1.7→47.181 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1832 3626 4.88 %
Rwork0.1494 70646 -
obs0.1511 74272 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.39 Å2 / Biso mean: 25.6471 Å2 / Biso min: 10.59 Å2
Refinement stepCycle: final / Resolution: 1.7→47.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6060 0 162 572 6794
Biso mean--31.79 37.57 -
Num. residues----777
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.72230.33541320.2688271596
1.7223-1.74590.33021470.2495267497
1.7459-1.77080.26311440.2297264397
1.7708-1.79730.28441690.2207269597
1.7973-1.82530.24111400.2136266398
1.8253-1.85530.26471530.204269797
1.8553-1.88730.21931290.1943268498
1.8873-1.92160.25061490.1823269797
1.9216-1.95850.23581430.1745266498
1.9585-1.99850.23311240.1579274097
1.9985-2.0420.17681210.1531268498
2.042-2.08950.18251520.1486271198
2.0895-2.14170.1981790.1421267998
2.1417-2.19960.17541660.1426268698
2.1996-2.26440.18621410.1346272398
2.2644-2.33740.19891100.139276199
2.3374-2.4210.17091150.1364275699
2.421-2.51790.1806980.14275499
2.5179-2.63250.2231270.1431277099
2.6325-2.77130.1681470.1432271199
2.7713-2.94490.17931090.1463277399
2.9449-3.17220.1861260.1488277399
3.1722-3.49130.18261310.1369274499
3.4913-3.99630.14921480.1278275099
3.9963-5.0340.14161680.1228274199
5.034-47.180.14481580.1508275898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.60590.21490.14050.42170.15790.5838-0.0215-0.0089-0.02260.01280.0132-0.01920.00840.03640.00620.15560.00330.00090.1611-0.00390.17459.954-18.16912.467
20.8443-0.2529-0.18050.66160.18750.5958-0.0036-0.04550.01130.04510.0083-0.0137-0.05060.0312-0.00980.204-0.0146-0.0060.160.01420.17532.4714.5629.761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:389 )A1 - 389
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:389 )B2 - 389

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