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- PDB-6nc7: Lipid II flippase MurJ, inward open conformation -

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Basic information

Entry
Database: PDB / ID: 6nc7
TitleLipid II flippase MurJ, inward open conformation
ComponentsLipid II flippase MurJ
KeywordsTRANSPORT PROTEIN / Transporter / Flippase / Peptidoglycan / Cell wall
Function / homologyPeptidoglycan biosynthesis protein MurJ / Lipid II flippase MurJ / lipid-linked peptidoglycan transporter activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / plasma membrane / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Lipid II flippase MurJ
Function and homology information
Biological speciesThermosipho africanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
B: Lipid II flippase MurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,86810
Polymers108,2762
Non-polymers2,5928
Water0
1
A: Lipid II flippase MurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3045
Polymers54,1381
Non-polymers1,1664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipid II flippase MurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5645
Polymers54,1381
Non-polymers1,4264
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.692, 105.514, 111.479
Angle α, β, γ (deg.)90.00, 125.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Lipid II flippase MurJ


Mass: 54137.957 Da / Num. of mol.: 2
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 / References: UniProt: B7IE18
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / Details: PEG400, ammonium sulfate

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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: 3→100 Å / Num. obs: 20396 / % possible obs: 99 % / Redundancy: 5.5 % / Net I/σ(I): 11.41
Reflection shellResolution: 3→3.1 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: 3→90.992 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.46
RfactorNum. reflection% reflection
Rfree0.2711 1027 5.04 %
Rwork0.2489 --
obs0.2499 20396 82.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→90.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7241 0 126 0 7367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057571
X-RAY DIFFRACTIONf_angle_d0.67910299
X-RAY DIFFRACTIONf_dihedral_angle_d16.2842512
X-RAY DIFFRACTIONf_chiral_restr0.0421233
X-RAY DIFFRACTIONf_plane_restr0.0061228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.15840.2601830.31981692X-RAY DIFFRACTION51
3.1584-3.35630.35791190.2952019X-RAY DIFFRACTION61
3.3563-3.61540.30271320.2842538X-RAY DIFFRACTION76
3.6154-3.97930.28391740.26113099X-RAY DIFFRACTION94
3.9793-4.55510.27711630.25163307X-RAY DIFFRACTION99
4.5551-5.73880.28851780.23693340X-RAY DIFFRACTION100
5.7388-91.03420.21281780.21373374X-RAY DIFFRACTION99

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