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- PDB-6e5d: Crystal structure of LpqN involved in cell envelope biogenesis of... -

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Basic information

Entry
Database: PDB / ID: 6e5d
TitleCrystal structure of LpqN involved in cell envelope biogenesis of Mycobacterium tuberculosis
ComponentsLipid binding protein LpqN
KeywordsLIPID BINDING PROTEIN / Mycobacterium tuberculosis cell envelope / 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 / Lipoprotein LpqN
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipid binding protein LpqN


Theoretical massNumber of molelcules
Total (without water)24,5271
Polymers24,5271
Non-polymers00
Water2,522140
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 area8870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.309, 55.521, 44.614
Angle α, β, γ (deg.)90.00, 103.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

21A-414-

HOH

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Components

#1: Protein Lipid binding protein LpqN


Mass: 24527.158 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.52 Å3/Da / Density % sol: 51.2 % / Description: Rhomboid crystals appeared in 3-5 days time.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M sodium citrate, pH 6.0, 1.5 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: 1.65→100 Å / Num. obs: 27327 / % possible obs: 96.1 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.02 / Rrim(I) all: 0.054 / Net I/σ(I): 19
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2452 / CC1/2: 0.956 / Rpim(I) all: 0.187 / Rrim(I) all: 0.465 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3177: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD-phased LpqN model

Resolution: 1.65→48.112 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.76
RfactorNum. reflection% reflection
Rfree0.2085 1289 4.73 %
Rwork0.1857 --
obs0.1868 27245 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→48.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 0 140 1431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021379
X-RAY DIFFRACTIONf_angle_d0.5451906
X-RAY DIFFRACTIONf_dihedral_angle_d14.787846
X-RAY DIFFRACTIONf_chiral_restr0.046219
X-RAY DIFFRACTIONf_plane_restr0.003258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.71610.32221230.25782645X-RAY DIFFRACTION88
1.7161-1.79420.26091470.25632893X-RAY DIFFRACTION97
1.7942-1.88880.33441340.25882855X-RAY DIFFRACTION95
1.8888-2.00710.25111610.22462884X-RAY DIFFRACTION98
2.0071-2.16210.24621510.20272949X-RAY DIFFRACTION98
2.1621-2.37970.23261160.20042924X-RAY DIFFRACTION96
2.3797-2.7240.23291570.20452894X-RAY DIFFRACTION97
2.724-3.43180.21651460.18322932X-RAY DIFFRACTION97
3.4318-48.13270.15431540.14892980X-RAY DIFFRACTION97
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)
14.5012-2.4399-2.07076.4024.97.3219-0.16070.58810.4949-0.29330.0844-0.8463-0.00081.4732-0.04330.2891-0.00380.08040.67810.11130.3599-135.6353-21.8071-175.4912
23.0088-1.45811.21653.3843-1.49135.9896-0.2297-0.36130.33120.55670.06860.2941-1.3068-0.22010.11980.37510.0297-0.00670.2629-0.0650.3272-150.1169-15.8165-157.7082
34.6835.3451-1.85116.4511-1.40096.8053-0.354-0.23310.01580.12910.0473-0.1668-0.46040.30010.25540.27440.0171-0.06770.2081-0.04510.2509-142.3259-18.7088-152.1073
43.0048-0.97522.00313.7665-2.54478.6352-0.2437-0.1070.20220.36860.0843-0.0903-0.29380.24730.1630.146-0.03-0.02060.1679-0.0170.207-142.0587-23.4438-156.9879
58.1009-4.11136.13334.5306-4.67286.85180.2020.4935-0.4944-0.3629-0.1797-0.08741.02070.8863-0.06890.45360.15690.07270.4264-0.02330.2543-139.6658-33.4686-169.9843
66.038-5.83654.56016.8818-4.71265.3290.23470.0162-0.1193-0.2669-0.17160.06180.53620.2072-0.03990.27790.0085-0.0110.1910.0070.17-145.2177-31.6928-164.5565
75.4474-3.3353.29696.3482-4.08386.103-0.1296-0.01350.08690.16110.0403-0.0793-0.0450.06590.18080.1657-0.0146-0.01710.1022-0.02570.1273-144.1474-26.7031-164.0464
84.1845-2.96444.09326.8348-5.38127.8324-0.0961-0.4616-0.23180.160.2710.47790.0972-0.3774-0.17670.2073-0.00810.02190.1864-0.02470.1913-148.613-27.811-158.0241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 105 )
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 133 )
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 157 )
6X-RAY DIFFRACTION6chain 'A' and (resid 158 through 178 )
7X-RAY DIFFRACTION7chain 'A' and (resid 179 through 194 )
8X-RAY DIFFRACTION8chain 'A' and (resid 195 through 228 )

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