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- PDB-6nc9: Lipid II flippase MurJ, outward-facing conformation -

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Basic information

Entry
Database: PDB / ID: 6nc9
TitleLipid II flippase MurJ, outward-facing conformation
ComponentsLipid II flippase MurJ
KeywordsTRANSPORT PROTEIN / Transporter / Flippase / Peptidoglycan / Cell wall
Function / homology
Function and homology information


lipid-linked peptidoglycan transporter activity / lipid translocation / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / plasma membrane
Similarity search - Function
Peptidoglycan biosynthesis protein MurJ / Lipid II flippase MurJ
Similarity search - Domain/homology
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Lipid II flippase MurJ
Similarity search - Component
Biological speciesThermosipho africanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKuk, A.C.Y. / Lee, S.-Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120594 United States
CitationJournal: Nat Commun / Year: 2019
Title: Visualizing conformation transitions of the Lipid II flippase MurJ.
Authors: Kuk, A.C.Y. / Hao, A. / Guan, Z. / Lee, S.Y.
History
DepositionDec 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: Lipid II flippase MurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,74718
Polymers54,1381
Non-polymers5,60917
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.579, 57.443, 86.406
Angle α, β, γ (deg.)90.00, 100.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lipid II flippase MurJ


Mass: 54137.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosipho africanus (strain TCF52B) (bacteria)
Strain: TCF52B / Gene: murJ, mviN, THA_1814 / Production host: Escherichia coli (E. coli) / References: UniProt: B7IE18

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Non-polymers , 5 types, 173 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.9 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / Details: PEG400-500, NaCl, pH 6.0-7.5 / PH range: 6.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 51025 / % possible obs: 99.9 % / Redundancy: 23.4 % / Net I/σ(I): 22.71
Reflection shellResolution: 1.8→1.9 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T77

5t77


Resolution: 1.8→84.897 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.81
RfactorNum. reflection% reflection
Rfree0.1997 2555 5.01 %
Rwork0.1797 --
obs0.1807 51025 88.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→84.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 294 156 4225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044165
X-RAY DIFFRACTIONf_angle_d0.6565570
X-RAY DIFFRACTIONf_dihedral_angle_d19.5351487
X-RAY DIFFRACTIONf_chiral_restr0.039640
X-RAY DIFFRACTIONf_plane_restr0.004656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83460.3016860.24821744X-RAY DIFFRACTION58
1.8346-1.87210.2696950.2471803X-RAY DIFFRACTION60
1.8721-1.91280.24561040.22421972X-RAY DIFFRACTION64
1.9128-1.95730.24221060.20862115X-RAY DIFFRACTION70
1.9573-2.00630.25051150.20212232X-RAY DIFFRACTION75
2.0063-2.06050.2011290.19472455X-RAY DIFFRACTION81
2.0605-2.12110.19991450.18942673X-RAY DIFFRACTION88
2.1211-2.18960.19871580.18732943X-RAY DIFFRACTION97
2.1896-2.26790.20751540.17243033X-RAY DIFFRACTION100
2.2679-2.35870.21091630.1573007X-RAY DIFFRACTION100
2.3587-2.4660.16981530.15183041X-RAY DIFFRACTION100
2.466-2.59610.17211700.15583032X-RAY DIFFRACTION100
2.5961-2.75870.16061640.14983026X-RAY DIFFRACTION100
2.7587-2.97170.17661580.16083045X-RAY DIFFRACTION100
2.9717-3.27080.19431590.17823058X-RAY DIFFRACTION100
3.2708-3.74410.19521450.18063079X-RAY DIFFRACTION100
3.7441-4.71710.21091780.18383065X-RAY DIFFRACTION100
4.7171-84.99120.20481730.1973147X-RAY DIFFRACTION100
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)
11.48390.01290.08860.7501-0.14310.756-0.0388-0.35260.02920.18250.1709-0.2402-0.0810.21870.21680.14520.0552-0.02530.0770.00750.0945-13.920523.132427.0655
22.0895-0.4483-0.27430.74960.52561.3622-0.0930.1364-0.10860.07840.01120.01290.1508-0.1126-0.02660.11980.00220.00480.02840.03780.1158-22.5313.387914.7668
30.5167-0.12520.26760.72460.26840.7941-0.12480.1619-0.0332-0.14880.04240.0440.0677-0.14720.01130.12980.0193-0.00260.1913-0.00210.1148-30.783224.321911.068
41.24860.46230.5711.0570.14631.69330.00330.20880.1366-0.0643-0.00960.0098-0.18240.0298-0.01530.10690.0715-0.01860.06760.02860.0607-20.330437.792718.0394
51.4783-0.72750.22741.96430.42861.6149-0.17410.00360.53240.1272-0.38070.4309-0.4489-0.4419-1.54120.22510.084-0.014-0.097-0.00470.1743-18.186848.061132.4982
61.1302-0.00521.15922.23730.20441.2141-0.10120.02170.03450.2145-0.02760.11770.1415-0.1763-0.00890.20210.01040.00070.0236-0.01960.0843-13.109839.488139.7207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 200 )
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 243 )
4X-RAY DIFFRACTION4chain 'A' and (resid 244 through 409 )
5X-RAY DIFFRACTION5chain 'A' and (resid 410 through 433 )
6X-RAY DIFFRACTION6chain 'A' and (resid 434 through 475 )

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