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- PDB-7ape: Crystal structure of LpqY from Mycobacterium thermoresistible in ... -

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Basic information

Entry
Database: PDB / ID: 7ape
TitleCrystal structure of LpqY from Mycobacterium thermoresistible in complex with trehalose
ComponentsLipoprotein (Sugar-binding) lpqY
KeywordsTRANSPORT PROTEIN / LpqY / ABC-transporter / trehalose complex / tuberculosis
Function / homology: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / trehalose / Lipoprotein (Sugar-binding) lpqY
Function and homology information
Biological speciesMycolicibacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFurze, C.M. / Guy, C.M. / Angula, J. / Cameron, A.D. / Fullam, E.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust104193/Z/14/Z United Kingdom
Wellcome Trust104193/Z/14/B United Kingdom
Royal Society104193/Z/14/Z United Kingdom
Royal Society104193/Z/14/B United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis of trehalose recognition by the mycobacterial LpqY-SugABC transporter.
Authors: Furze, C.M. / Delso, I. / Casal, E. / Guy, C.S. / Seddon, C. / Brown, C.M. / Parker, H.L. / Radhakrishnan, A. / Pacheco-Gomez, R. / Stansfeld, P.J. / Angulo, J. / Cameron, A.D. / Fullam, E.
History
DepositionOct 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 1, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein (Sugar-binding) lpqY
B: Lipoprotein (Sugar-binding) lpqY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2554
Polymers97,5712
Non-polymers6852
Water10,034557
1
A: Lipoprotein (Sugar-binding) lpqY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1282
Polymers48,7851
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipoprotein (Sugar-binding) lpqY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1282
Polymers48,7851
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint5 kcal/mol
Surface area31010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.361, 92.361, 216.577
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-771-

HOH

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Components

#1: Protein Lipoprotein (Sugar-binding) lpqY


Mass: 48785.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium thermoresistibile (bacteria)
Gene: RMCT_2827 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A100XFZ4
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Hepes pH 6.0, 50 % w/v polypropylene glycol 400, 5 % DMSO, 1 mM TCEP

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.7→54.1 Å / Num. obs: 102435 / % possible obs: 98.7 % / Redundancy: 23 % / Biso Wilson estimate: 26.14 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.16
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9278 / Rpim(I) all: 0.57

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Processing

Software
NameVersionClassification
PHASERphasing
XDSdata scaling
XDSdata reduction
PHENIX1.15.2refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LpqY iodide soak

Resolution: 1.7→48.4 Å / SU ML: 0.2054 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1959 5141 5.02 %
Rwork0.1687 97271 -
obs0.17 102412 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.75 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 46 557 7262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016850
X-RAY DIFFRACTIONf_angle_d1.05959361
X-RAY DIFFRACTIONf_chiral_restr0.0571071
X-RAY DIFFRACTIONf_plane_restr0.00871247
X-RAY DIFFRACTIONf_dihedral_angle_d4.45234889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.32781540.31512861X-RAY DIFFRACTION87.7
1.74-1.760.31091660.2822999X-RAY DIFFRACTION93.39
1.76-1.780.29541440.2613139X-RAY DIFFRACTION95.77
1.78-1.810.29231760.24733109X-RAY DIFFRACTION97.02
1.81-1.830.28461930.23923157X-RAY DIFFRACTION98.27
1.83-1.860.26481800.22223183X-RAY DIFFRACTION99
1.86-1.880.26021620.21683289X-RAY DIFFRACTION99.6
1.88-1.910.22441720.20693223X-RAY DIFFRACTION100
1.91-1.950.23641820.19733210X-RAY DIFFRACTION100
1.95-1.980.23151800.19033252X-RAY DIFFRACTION100
1.98-2.010.24931500.19163254X-RAY DIFFRACTION99.94
2.01-2.050.23991940.17833236X-RAY DIFFRACTION99.94
2.05-2.10.20871690.17463250X-RAY DIFFRACTION99.85
2.1-2.140.20571670.17343270X-RAY DIFFRACTION99.94
2.14-2.190.22641820.16713243X-RAY DIFFRACTION99.97
2.19-2.250.19911600.16623272X-RAY DIFFRACTION99.97
2.25-2.310.17531640.1623268X-RAY DIFFRACTION99.94
2.31-2.370.21991750.16623282X-RAY DIFFRACTION100
2.37-2.450.19511780.15813245X-RAY DIFFRACTION99.97
2.45-2.540.19771720.16243276X-RAY DIFFRACTION100
2.54-2.640.20781950.16183290X-RAY DIFFRACTION100
2.64-2.760.21311630.16083296X-RAY DIFFRACTION100
2.76-2.910.18641920.16423298X-RAY DIFFRACTION100
2.91-3.090.17561610.16723329X-RAY DIFFRACTION99.97
3.09-3.330.17221840.16033304X-RAY DIFFRACTION100
3.33-3.660.18691670.1533351X-RAY DIFFRACTION100
3.66-4.190.16911570.14453390X-RAY DIFFRACTION100
4.19-5.280.15651840.13793415X-RAY DIFFRACTION100

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