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- PDB-6nc6: Lipid II flippase MurJ, inward closed conformation -

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Basic information

Entry
Database: PDB / ID: 6nc6
TitleLipid II flippase MurJ, inward closed conformation
ComponentsLipid II flippase MurJ
KeywordsTRANSPORT PROTEIN / Transporter / Flippase / Peptidoglycan / Cell wall
Function / homology
Function and homology information


lipid-linked peptidoglycan transporter activity / 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 / Lipid II flippase MurJ
Similarity search - Component
Biological speciesThermosipho africanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 10, 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)108,99912
Polymers108,2762
Non-polymers72310
Water00
1
A: Lipid II flippase MurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6897
Polymers54,1381
Non-polymers5516
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipid II flippase MurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3105
Polymers54,1381
Non-polymers1724
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.134, 101.759, 158.516
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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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 (E. coli) / References: UniProt: B7IE18
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4

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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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase / pH: 4.6 / Details: 1 M NaCl, 50 mM Na acetate-HCl pH 4.6, 40% PEG400

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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: 3.2→100 Å / Num. obs: 17624 / % possible obs: 99.4 % / Redundancy: 20.7 % / Net I/σ(I): 9.48
Reflection shellResolution: 3.2→3.3 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: 3.2→85.633 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.29
RfactorNum. reflection% reflection
Rfree0.2779 876 4.97 %
Rwork0.2547 --
obs0.2559 17624 89.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→85.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7292 0 27 0 7319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047531
X-RAY DIFFRACTIONf_angle_d0.6310236
X-RAY DIFFRACTIONf_dihedral_angle_d14.7772538
X-RAY DIFFRACTIONf_chiral_restr0.0431226
X-RAY DIFFRACTIONf_plane_restr0.0051223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.40050.33711110.2892091X-RAY DIFFRACTION69
3.4005-3.66310.24971200.26982350X-RAY DIFFRACTION77
3.6631-4.03170.2751520.25212873X-RAY DIFFRACTION94
4.0317-4.61510.29131570.26563038X-RAY DIFFRACTION98
4.6151-5.81430.3141640.25453121X-RAY DIFFRACTION100
5.8143-85.66350.23221720.22643275X-RAY DIFFRACTION100

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