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- PDB-6hsy: Two-phospholipid-bound crystal structure of the substrate-binding... -

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Basic information

Entry
Database: PDB / ID: 6hsy
TitleTwo-phospholipid-bound crystal structure of the substrate-binding protein Ttg2D from Pseudomonas aeruginosa
ComponentsToluene tolerance protein Ttg2D
KeywordsLIPID TRANSPORT / substrate-binding protein / two diacyl lipids / Ttg2D / MlaC
Function / homology
Function and homology information


Tgt2/MlaC / Tgt2/MlaC superfamily / Toluene tolerance Ttg2/phospholipid-binding protein MlaC / MlaC protein / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Phospholipid PG(16:0/cy17:0) / Phospholipid PG(16:0/cy17:0) / Toluene tolerance protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsCostenaro, L. / Conchillo-Sole, O. / Daura, X.
Funding support Spain, 2items
OrganizationGrant numberCountry
European UnionFP7 HEALTH-F3-2009-223101 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBIO2015-66674-R Spain
CitationJournal: Commun Biol / Year: 2021
Title: The Pseudomonas aeruginosa substrate-binding protein Ttg2D functions as a general glycerophospholipid transporter across the periplasm.
Authors: Yero, D. / Diaz-Lobo, M. / Costenaro, L. / Conchillo-Sole, O. / Mayo, A. / Ferrer-Navarro, M. / Vilaseca, M. / Gibert, I. / Daura, X.
History
DepositionOct 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toluene tolerance protein Ttg2D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9588
Polymers23,0161
Non-polymers1,9427
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-28 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.639, 124.639, 38.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Toluene tolerance protein Ttg2D


Mass: 23016.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Expression tags:N-term: MC-term: KLAAALEHHHHHH / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA4453 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HVW4

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Non-polymers , 5 types, 28 molecules

#2: Chemical ChemComp-GOT / Phospholipid PG(16:0/cy17:0)


Mass: 734.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H75O10P
#3: Chemical ChemComp-H3T / Phospholipid PG(16:0/cy17:0)


Mass: 734.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H75O10P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 3.71 Å3/Da / Density % sol: 66.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.17 M Ammonium sulfate, 25.5% w/v PEG 4000, 15% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.980227 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2013
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980227 Å / Relative weight: 1
ReflectionResolution: 2.53→62.32 Å / Num. obs: 11489 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 51.33 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.053 / Rrim(I) all: 0.135 / Net I/σ(I): 8.2
Reflection shellResolution: 2.53→2.64 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 2 / Num. unique obs: 1349 / CC1/2: 0.717 / Rpim(I) all: 0.352 / Rrim(I) all: 0.795 / % possible all: 98

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Processing

Software
NameVersionClassification
iMOSFLM1.0.7data reduction
Aimless0.1.27data scaling
PHASER2.5.1phasing
PHENIX1.14rc1_3161refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Poly-A homology model based on 2QGU

2qgu


Resolution: 2.53→62.32 Å / SU ML: 0.3451 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.8051 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 582 5.08 %Random
Rwork0.2093 ---
obs0.2113 11462 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.04 Å2
Refinement stepCycle: LAST / Resolution: 2.53→62.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 0 127 21 1629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00281679
X-RAY DIFFRACTIONf_angle_d0.47352260
X-RAY DIFFRACTIONf_chiral_restr0.0386242
X-RAY DIFFRACTIONf_plane_restr0.0021285
X-RAY DIFFRACTIONf_dihedral_angle_d16.7165678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.780.34591320.29782661X-RAY DIFFRACTION98.66
2.78-3.190.28361530.23042721X-RAY DIFFRACTION99.31
3.19-4.020.25121410.19732709X-RAY DIFFRACTION99.79
4.02-62.340.22181560.19242789X-RAY DIFFRACTION99.39

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