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- PDB-7wda: Crystal structure LpqY in complex with Trehalose from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 7wda
TitleCrystal structure LpqY in complex with Trehalose from Mycobacterium tuberculosis
ComponentsTrehalose-binding lipoprotein LpqY
KeywordsSUGAR BINDING PROTEIN / Mycobacterium tuberculosis / LpqY / Trehalose / SugABC
Function / homology
Function and homology information


trehalose transmembrane transporter activity / trehalose transport / biological process involved in interaction with host / ATP-binding cassette (ABC) transporter complex / periplasmic space / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
trehalose / Trehalose-binding lipoprotein LpqY
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsSharma, D. / Das, U.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical ResearchICMR-12(26)/2020 India
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural analysis of LpqY, a substrate-binding protein from the SugABC transporter of Mycobacterium tuberculosis, provides insights into its trehalose specificity.
Authors: Sharma, D. / Singh, M. / Kaur, P. / Das, U.
History
DepositionDec 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 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.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 13, 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_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 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: Trehalose-binding lipoprotein LpqY
B: Trehalose-binding lipoprotein LpqY
C: Trehalose-binding lipoprotein LpqY
D: Trehalose-binding lipoprotein LpqY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,16612
Polymers189,4124
Non-polymers1,7538
Water16,952941
1
A: Trehalose-binding lipoprotein LpqY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7913
Polymers47,3531
Non-polymers4382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trehalose-binding lipoprotein LpqY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7913
Polymers47,3531
Non-polymers4382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Trehalose-binding lipoprotein LpqY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8884
Polymers47,3531
Non-polymers5343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Trehalose-binding lipoprotein LpqY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6952
Polymers47,3531
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.304, 162.135, 142.796
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

#1: Protein
Trehalose-binding lipoprotein LpqY


Mass: 47353.098 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: lpqY, Rv1235 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WGU9
#2: Polysaccharide
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 941 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2021 / Details: Vertical CRL / Horizontal Eliptical mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.91→48.03 Å / Num. obs: 137970 / % possible obs: 99.52 % / Redundancy: 12.9 % / Biso Wilson estimate: 33.12 Å2 / CC1/2: 0.998 / CC star: 0.99 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.07 / Net I/σ(I): 8.43
Reflection shellResolution: 1.91→1.97 Å / Redundancy: 11.6 % / Rmerge(I) obs: 4.29 / Mean I/σ(I) obs: 0.54 / Num. unique obs: 13670 / CC1/2: 0.279 / Rpim(I) all: 1.3 / % possible all: 95.83

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WCJ

7wcj


Resolution: 1.91→48.03 Å / SU ML: 0.2805 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.1014
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 1994 1.45 %RANDOM
Rwork0.1993 135348 --
obs0.1996 137342 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.25 Å2
Refinement stepCycle: LAST / Resolution: 1.91→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12941 0 112 943 13996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003913388
X-RAY DIFFRACTIONf_angle_d0.664118353
X-RAY DIFFRACTIONf_chiral_restr0.04512123
X-RAY DIFFRACTIONf_plane_restr0.00642416
X-RAY DIFFRACTIONf_dihedral_angle_d12.59344713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.960.43231120.39968817X-RAY DIFFRACTION91.45
1.96-2.010.37111530.34639570X-RAY DIFFRACTION99.48
2.01-2.070.35071470.30619660X-RAY DIFFRACTION99.84
2.07-2.140.29431370.27889683X-RAY DIFFRACTION99.93
2.14-2.210.27821490.25179648X-RAY DIFFRACTION99.96
2.21-2.30.23971410.2329669X-RAY DIFFRACTION99.93
2.3-2.40.25431410.2219664X-RAY DIFFRACTION99.98
2.4-2.530.241450.20459721X-RAY DIFFRACTION99.98
2.53-2.690.251430.19739692X-RAY DIFFRACTION100
2.69-2.90.22211490.18829744X-RAY DIFFRACTION99.99
2.9-3.190.21441390.18759780X-RAY DIFFRACTION100
3.19-3.650.17761430.16889765X-RAY DIFFRACTION100
3.65-4.60.16541420.15719844X-RAY DIFFRACTION100
4.6-48.030.20351530.186410091X-RAY DIFFRACTION99.84
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)
11.60983807853-0.3354962685490.3331729510020.592423644776-0.1692682780550.7671099038340.06560255657510.1219097282880.0881532497608-0.110211915949-0.04366765500590.0414809006601-0.0148888085748-0.0595840371947-0.02219318040540.2173196861890.04071977610850.0009563306963670.211803084670.01089378735140.4573479120334.90821373125.3829999563622.1165014585
20.9438996902890.00602582729773-0.1054326671891.04507580205-0.1852518095290.56079965810.00488598521611-0.0237511192462-0.06245331814770.08168177128970.03247766210550.102391915776-0.00117352778716-0.0534780208573-0.03497816541260.190307445388-0.0006882292170910.0178206902010.1713081802890.004438000573120.41866231310335.6262371215-4.5637330357754.663701507
30.6844578624830.04983249015860.01767764701141.920237257040.1598660231180.55477971598-0.05969405887140.1441720845860.0311939055475-0.1694829217150.1007822735290.0608353279430.0146932512498-0.020012218161-0.03764937554020.215796859454-0.04038552641670.04223797678550.2639943094090.01074662821760.43209903572873.587469315936.960351288957.6031300984
40.745929292618-0.1186757181890.07351681044721.01697452694-0.1289745093240.457621912543-0.0171442167428-0.06940345552330.04062442764690.03400811427460.035057945704-0.157722424497-0.01035578164580.0329857890064-0.01898489582470.1610309406770.005282529910160.0172332281190.210235045719-0.01376729225890.41909631276381.551277917636.374416670890.6404087133
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 32 through 501)AA - B32 - 5011
22(chain 'B' and resid 31 through 501)BC - D31 - 5011
33(chain 'C' and resid 32 through 501)CE - F32 - 5011
44(chain 'D' and resid 31 through 464)DG31 - 4641 - 426

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