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- PDB-7waw: MurJ inward closed form -

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Basic information

Entry
Database: PDB / ID: 7waw
TitleMurJ inward closed form
Componentslipid II flippase MurJ
KeywordsLIPID TRANSPORT / 14 transmembrane helices / inner membrane / Lipid II / MOP superfamily
Function / homology(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Function and homology information
Biological speciesArsenophonus endosymbiont of Nilaparvata lugens (Arsenophonus endosymbiont of Nilaparvata lugens)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 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 15, 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)58,0626
Polymers56,2791
Non-polymers1,7835
Water55831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22550 Å2
Unit cell
Length a, b, c (Å)56.410, 71.460, 74.540
Angle α, β, γ (deg.)90.00, 96.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein lipid II flippase MurJ


Mass: 56279.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arsenophonus endosymbiont of Nilaparvata lugens (Arsenophonus endosymbiont of Nilaparvata lugens)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / Details: MPD, MgCl2, Tris-HCl / PH range: 8.9-9.3

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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: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→44.07 Å / Num. obs: 14632 / % possible obs: 99.95 % / Redundancy: 12.3 % / CC1/2: 0.944 / Net I/σ(I): 3.75
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 1450 / CC1/2: 0.684

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Processing

SoftwareName: PHENIX / Version: (1.18.2_3874: ???) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.8→44.07 Å / SU ML: 0.38 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 1463 10 %
Rwork0.2164 --
obs0.2221 14629 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3851 0 111 31 3993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074050
X-RAY DIFFRACTIONf_angle_d1.0325480
X-RAY DIFFRACTIONf_dihedral_angle_d20.937623
X-RAY DIFFRACTIONf_chiral_restr0.054653
X-RAY DIFFRACTIONf_plane_restr0.006655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90.32431450.251305X-RAY DIFFRACTION100
2.9-3.020.33671430.25851290X-RAY DIFFRACTION100
3.02-3.150.30671460.25351310X-RAY DIFFRACTION100
3.15-3.320.29571460.22581324X-RAY DIFFRACTION100
3.32-3.530.26351460.21451318X-RAY DIFFRACTION100
3.53-3.80.26961460.20791306X-RAY DIFFRACTION100
3.8-4.180.25791450.20371309X-RAY DIFFRACTION100
4.18-4.790.2491460.18871319X-RAY DIFFRACTION100
4.79-6.030.27611480.23031328X-RAY DIFFRACTION100
6.03-44.070.2421520.20031357X-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)
13.3206-0.0827-0.68520.33430.27540.87010.1532-0.00860.1066-0.0967-0.05880.270.0183-0.0473-0.07780.12640.01670.01250.2113-0.04590.2681-4.02994.5502-7.1537
22.1184-0.8807-0.92522.18020.36181.22070.1033-0.1607-0.0097-0.0093-0.15010.22310.04080.02360.02130.0566-0.0148-0.03850.2594-0.00750.1958-2.48216.8564-7.8464
30.6276-0.69811.20712.31580.24571.54870.0364-0.3534-0.3118-0.05390.01760.7008-0.0028-0.5867-0.02880.24810.00580.07330.4170.06820.3445-3.97573.4102-29.848
41.50630.16380.08873.1337-1.24411.9507-0.04130.12070.0613-0.24220.11550.32980.1636-0.272-0.04210.2366-0.00040.05080.2186-0.10310.12021.34072.0999-35.1292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 120 )
2X-RAY DIFFRACTION2chain 'A' and (resid 121 through 286 )
3X-RAY DIFFRACTION3chain 'A' and (resid 287 through 380 )
4X-RAY DIFFRACTION4chain 'A' and (resid 381 through 503 )

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