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- PDB-6e5f: Crystal structure of LpqN involved in cell envelope biogenesis of... -

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Basic information

Entry
Database: PDB / ID: 6e5f
TitleCrystal structure of LpqN involved in cell envelope biogenesis of Mycobacterium tuberculosis
ComponentsLipid binding protein LpqN
KeywordsLIPID BINDING PROTEIN / (6DDTre)Lauryl-6-Trehaloside
Function / homologyLipoprotein LpqN/LpqT-like / Probable lipoprotein LpqN / peptidoglycan-based cell wall / cell wall organization / Prokaryotic membrane lipoprotein lipid attachment site profile. / extracellular region / plasma membrane / Chem-L6T / Lipoprotein LpqN
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsRajavel, M. / Su, C.C. / Yu, E.W.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural and functional evidence that lipoprotein LpqN supports cell envelope biogenesis inMycobacterium tuberculosis.
Authors: Melly, G.C. / Stokas, H. / Dunaj, J.L. / Hsu, F.F. / Rajavel, M. / Su, C.C. / Yu, E.W. / Purdy, G.E.
History
DepositionJul 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Lipid binding protein LpqN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2092
Polymers23,6981
Non-polymers5111
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.004, 80.004, 59.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

21A-494-

HOH

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Components

#1: Protein Lipid binding protein LpqN


Mass: 23698.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: lpqN, Rv0583c / Plasmid: pET-mod / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O53780
#2: Sugar ChemComp-L6T / alpha-D-glucopyranosyl 6-O-dodecyl-alpha-D-glucopyranoside


Type: saccharide / Mass: 510.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C24H46O11
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2 Å3/Da / Density % sol: 38.56 % / Description: Needle-like crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium citrate, pH 6.5, 1.9 M ammonium sulfate
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2018
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.35→56.571 Å / Num. obs: 40174 / % possible obs: 98.4 % / Redundancy: 8.4 % / Biso Wilson estimate: 20.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.021 / Rrim(I) all: 0.062 / Net I/σ(I): 18.2
Reflection shellResolution: 1.35→1.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.264 / Rpim(I) all: 0.806 / Rrim(I) all: 1.51 / % possible all: 70.6

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Processing

Software
NameVersionClassification
PHENIX1.14rc1_3177refinement
PHENIX1.14rc1_3177refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6E5D

6e5d


Resolution: 1.37→56.57 Å / SU ML: 0.1682 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.0121
RfactorNum. reflection% reflection
Rfree0.2035 1812 4.62 %
Rwork0.1768 --
obs0.178 39223 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.4 Å2
Refinement stepCycle: LAST / Resolution: 1.37→56.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 35 107 1433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441408
X-RAY DIFFRACTIONf_angle_d0.76381946
X-RAY DIFFRACTIONf_chiral_restr0.0659232
X-RAY DIFFRACTIONf_plane_restr0.0041254
X-RAY DIFFRACTIONf_dihedral_angle_d18.3082575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.410.31481130.33462860X-RAY DIFFRACTION98.02
1.41-1.450.33921260.2682874X-RAY DIFFRACTION99.47
1.45-1.50.2641190.2352856X-RAY DIFFRACTION99.87
1.5-1.550.24551630.21292870X-RAY DIFFRACTION100
1.55-1.610.22671640.1992843X-RAY DIFFRACTION99.9
1.61-1.680.24041310.20272896X-RAY DIFFRACTION99.97
1.68-1.770.24841320.20592881X-RAY DIFFRACTION99.97
1.77-1.880.22331490.19892867X-RAY DIFFRACTION99.97
1.88-2.030.1951280.17822876X-RAY DIFFRACTION99.87
2.03-2.230.18621680.17522852X-RAY DIFFRACTION100
2.23-2.560.20151400.17732900X-RAY DIFFRACTION99.97
2.56-3.220.19251630.17642863X-RAY DIFFRACTION99.97
3.22-56.620.19021160.15322973X-RAY DIFFRACTION99.77
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)
11.781414109610.712899812013-0.05613007769634.838938840741.067550193223.68547026187-0.189673408409-0.108427313185-0.02127627318560.1500721877880.364945989781-0.09292376912270.1301515668030.409714447726-0.1135023079230.1343347044910.071565352045-0.002354925827280.308556835938-0.02613399607640.196326505491-26.1869611173-4.8075317856920.2729971172
25.08375606585.00404663614.391458126676.979332594684.717727413624.018936729860.0580901917947-0.203552611166-0.2831739338930.2178204546160.227433679112-0.3937974212940.4216862435580.742658914419-0.1546336032080.3694842337660.2243073308660.02534160220440.2309603022460.07315706409720.189053388937-25.1077284612-19.76099411620.3214885263
31.5981397605-1.18396864082-0.4881284163236.700583871922.358957014253.215852678220.0470987149357-0.146237737742-0.175698330507-0.03374676506340.0467493100108-0.1471159376180.6703426827980.419745196894-0.09807913700270.3279708718320.131442810098-0.02343111240520.2116819171180.02215918572910.172850868966-25.4924455794-15.329763507615.140840706
46.92058456923-2.56285977507-2.468586329685.321282395713.324899004357.052587619070.145187514657-0.1488703516950.0123877733136-0.7501657490480.162496371733-0.319651527363-0.7651288865371.36977699869-0.1972981832360.238697689956-0.03283002306330.01257425515290.2782445678330.02335098971340.199073857096-24.3001418968-1.747109882855.95694864518
52.45560453689-0.834823632861-0.9137378499392.12105349512.027945732971.89881375087-0.168459551066-0.347158083699-0.383399306265-0.05374963456860.177067765590.1893826418490.3982202169240.5396286961530.07245941466710.2198024485030.0987967925089-0.01891988798410.1843193252160.008724424862430.199149397423-28.8767018378-7.987783294387.26005193219
62.41207442943-1.85076905559-1.897309097253.340984679512.650509202514.739977928670.02399274506960.0818895575787-0.1477652207570.0358862628781-0.0115681378620.08997170041860.5020631061090.02091261464790.01362065513920.2239458270830.057340154649-0.02447278052760.1411532868460.02211409812320.147862143254-31.0568552476-12.504094479211.5109682876
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 92 )
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 105 )
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 133 )
4X-RAY DIFFRACTION4chain 'A' and (resid 134 through 157 )
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 178 )
6X-RAY DIFFRACTION6chain 'A' and (resid 179 through 228 )

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