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- PDB-7yle: RnDmpX in complex with DMSP -

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Basic information

Entry
Database: PDB / ID: 7yle
TitleRnDmpX in complex with DMSP
ComponentsGlycine betaine/proline ABC transporter, periplasmic glycinebetaine/proline-binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter / substrate binding protein
Function / homologyABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid / Glycine betaine/proline ABC transporter, periplasmic glycinebetaine/proline-binding protein
Function and homology information
Biological speciesRoseovarius nubinhibens ISM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.052 Å
AuthorsLi, C.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Isme J / Year: 2023
Title: Ubiquitous occurrence of a dimethylsulfoniopropionate ABC transporter in abundant marine bacteria.
Authors: Li, C.Y. / Mausz, M.A. / Murphy, A. / Zhang, N. / Chen, X.L. / Wang, S.Y. / Gao, C. / Aguilo-Ferretjans, M.M. / Silvano, E. / Lidbury, I.D.E.A. / Fu, H.H. / Todd, J.D. / Chen, Y. / Zhang, Y.Z.
History
DepositionJul 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycine betaine/proline ABC transporter, periplasmic glycinebetaine/proline-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4662
Polymers34,3301
Non-polymers1361
Water4,774265
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)74.332, 74.332, 87.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Glycine betaine/proline ABC transporter, periplasmic glycinebetaine/proline-binding protein


Mass: 34330.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseovarius nubinhibens ISM (bacteria) / Gene: ISM_12265 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3SME7
#2: Chemical ChemComp-DQY / 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid


Mass: 136.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 3.53 Å3/Da / Density % sol: 65.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M magnesium chloride, 0.1M Bis-Tris (pH 5.5), 25% (wt/vol) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.989 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 29829 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 31.77 Å2 / Rmerge(I) obs: 0.07 / Χ2: 1.65 / Net I/σ(I): 10.9 / Num. measured all: 222723
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.05-2.127.50.51429741.0461100
2.12-2.217.50.43929571.1361100
2.21-2.317.50.30729541.5161100
2.31-2.437.50.22829861.1661100
2.43-2.587.50.17629631.4181100
2.58-2.787.50.1429721.8171100
2.78-3.067.40.1129772.3051100
3.06-3.517.30.07430102.5171100
3.51-4.427.40.04530032.0431100
4.42-507.60.03430331.573199.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.052→31.088 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2222 1439 5.08 %
Rwork0.1865 26872 -
obs0.1883 28311 94.66 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.84 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 91.24 Å2 / Biso mean: 38.63 Å2 / Biso min: 20.17 Å2
Baniso -1Baniso -2Baniso -3
1--3.0743 Å2-0 Å20 Å2
2---3.0743 Å2-0 Å2
3---6.1485 Å2
Refinement stepCycle: final / Resolution: 2.052→31.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2257 0 8 265 2530
Biso mean--26.74 43.6 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072325
X-RAY DIFFRACTIONf_angle_d1.0543185
X-RAY DIFFRACTIONf_chiral_restr0.069356
X-RAY DIFFRACTIONf_plane_restr0.005416
X-RAY DIFFRACTIONf_dihedral_angle_d13.429794
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.052-2.12490.31181350.2263242486
2.1249-2.210.31331240.2209244186
2.21-2.31050.28181360.2471251489
2.3105-2.43230.26511440.218265194
2.4323-2.58460.24681290.2105273896
2.5846-2.7840.24961560.2215274998
2.784-3.0640.27261520.2143279699
3.064-3.50680.20561710.1944282499
3.5068-4.41620.19881580.154283699
4.4162-31.0880.16991340.15352899100

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