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- PDB-7wag: Crystal structure of MurJ squeezed form -

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Basic information

Entry
Database: PDB / ID: 7wag
TitleCrystal structure of MurJ squeezed form
ComponentsLipid II flippase MurJ
KeywordsLIPID TRANSPORT / 14 transmembrane helices / inner membrane / Lipid II / MOP superfamily
Function / homology
Function and homology information


glycolipid translocation / lipid-linked peptidoglycan transport / division septum / lipid-linked peptidoglycan transporter activity / lipid translocation / cardiolipin binding / 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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Lipid II flippase MurJ
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsTsukazaki, T. / Kohga, H. / Tanaka, Y. / Yoshikaie, K. / Taniguchi, K. / Fujimoto, K.
Funding support Japan, 7items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21H05155 Japan
Japan Society for the Promotion of Science (JSPS)JP21H05153 Japan
Japan Society for the Promotion of Science (JSPS)21K19226 Japan
Japan Society for the Promotion of Science (JSPS)21KK0125 Japan
Japan Society for the Promotion of Science (JSPS)19K22395 Japan
Japan Society for the Promotion of Science (JSPS)18KK0197 Japan
Japan Society for the Promotion of Science (JSPS)18H02405 Japan
CitationJournal: Structure / Year: 2022
Title: Crystal structure of the lipid flippase MurJ in a "squeezed" form distinct from its inward- and outward-facing forms.
Authors: Kohga, H. / Mori, T. / Tanaka, Y. / Yoshikaie, K. / Taniguchi, K. / Fujimoto, K. / Fritz, L. / Schneider, T. / Tsukazaki, T.
History
DepositionDec 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 17, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipid II flippase MurJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,32115
Polymers56,5791
Non-polymers4,74114
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-27 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.450, 75.060, 115.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lipid II flippase MurJ / Peptidoglycan biosynthesis protein MurJ


Mass: 56579.410 Da / Num. of mol.: 1 / Mutation: v10R, S11C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: murJ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AF16
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / Details: MPD, MgCl2, Tris-HCl, PEG, OLC

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.55→45.7 Å / Num. obs: 21690 / % possible obs: 99.93 % / Redundancy: 35.7 % / CC1/2: 0.996 / Net I/σ(I): 10.98
Reflection shellResolution: 2.55→2.64 Å / Num. unique obs: 2154 / CC1/2: 0.502 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Cootmodel building
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CC4

6cc4


Resolution: 2.55→45.7 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 26.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 2004 9.24 %
Rwork0.2145 --
obs0.2195 21682 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 201 60 4273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044294
X-RAY DIFFRACTIONf_angle_d0.7785763
X-RAY DIFFRACTIONf_dihedral_angle_d15.692728
X-RAY DIFFRACTIONf_chiral_restr0.048673
X-RAY DIFFRACTIONf_plane_restr0.006683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.33991370.29391389X-RAY DIFFRACTION100
2.61-2.680.30061470.2591388X-RAY DIFFRACTION100
2.68-2.760.31641360.2311375X-RAY DIFFRACTION100
2.76-2.850.28671390.22571391X-RAY DIFFRACTION100
2.85-2.950.29611380.22211386X-RAY DIFFRACTION100
2.95-3.070.28721400.2241372X-RAY DIFFRACTION100
3.07-3.210.27621420.21341400X-RAY DIFFRACTION100
3.21-3.380.2861420.20271400X-RAY DIFFRACTION100
3.38-3.590.24821440.19881391X-RAY DIFFRACTION100
3.59-3.870.23611380.19661395X-RAY DIFFRACTION100
3.87-4.260.24641480.19751418X-RAY DIFFRACTION100
4.26-4.880.23371490.20911415X-RAY DIFFRACTION100
4.88-6.140.27861450.24191443X-RAY DIFFRACTION100
6.14-45.70.28531590.2021515X-RAY DIFFRACTION100

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