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- PDB-6cc4: Structure of MurJ from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 6cc4
TitleStructure of MurJ from Escherichia coli
Componentssoluble cytochrome b562, lipid II flippase MurJ chimera
KeywordsTRANSPORT PROTEIN / Lipid II flippase / MOP superfamily / Peptidoglycan synthesis
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 / electron transport chain / cell wall organization / regulation of cell shape ...glycolipid translocation / lipid-linked peptidoglycan transport / division septum / lipid-linked peptidoglycan transporter activity / lipid translocation / cardiolipin binding / peptidoglycan biosynthetic process / electron transport chain / cell wall organization / regulation of cell shape / periplasmic space / electron transfer activity / iron ion binding / heme binding / plasma membrane
Similarity search - Function
Peptidoglycan biosynthesis protein MurJ / Lipid II flippase MurJ / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
PHOSPHATE ION / Soluble cytochrome b562 / Lipid II flippase MurJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsZheng, S. / Kruse, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI109764 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure and mutagenic analysis of the lipid II flippase MurJ fromEscherichia coli.
Authors: Zheng, S. / Sham, L.T. / Rubino, F.A. / Brock, K.P. / Robins, W.P. / Mekalanos, J.J. / Marks, D.S. / Bernhardt, T.G. / Kruse, A.C.
History
DepositionFeb 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

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Assembly

Deposited unit
A: soluble cytochrome b562, lipid II flippase MurJ chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8332
Polymers66,7381
Non-polymers951
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-6 kcal/mol
Surface area28960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.954, 118.036, 128.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein soluble cytochrome b562, lipid II flippase MurJ chimera / Cytochrome b-562 / Peptidoglycan biosynthesis protein MurJ


Mass: 66737.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC, murJ, mviN, yceN, b1069, JW1056
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0ABE7, UniProt: P0AF16
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 100 mM MES, pH 6.0, 100 mM potassium phosphate dibasic, 28% PEG300, 1% 1,2,3-heptanetriol, lipid stock used for reconstitution was 10:1 w/w monoolein:cholesterol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2015
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 10739 / % possible obs: 95.5 % / Redundancy: 2.7 % / CC1/2: 0.953 / Rmerge(I) obs: 0.342 / Rpim(I) all: 0.229 / Rrim(I) all: 0.415 / Χ2: 1.135 / Net I/av σ(I): 3.57 / Net I/σ(I): 3.57
Reflection shellResolution: 3.5→3.58 Å / Redundancy: 2.4 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 0.66 / Num. unique obs: 718 / CC1/2: 0.211 / Rpim(I) all: 1.131 / Rrim(I) all: 1.926 / Χ2: 1.04 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5T77

5t77


Resolution: 3.5→35.715 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.47
RfactorNum. reflection% reflectionSelection details
Rfree0.3013 513 4.82 %Random selection
Rwork0.2799 ---
obs0.281 10640 94.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 74.8 Å2
Refinement stepCycle: LAST / Resolution: 3.5→35.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4603 0 5 0 4608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034710
X-RAY DIFFRACTIONf_angle_d0.746411
X-RAY DIFFRACTIONf_dihedral_angle_d15.8712793
X-RAY DIFFRACTIONf_chiral_restr0.041771
X-RAY DIFFRACTIONf_plane_restr0.008791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.85190.40211250.34162494X-RAY DIFFRACTION95
3.8519-4.40840.30571400.28442556X-RAY DIFFRACTION97
4.4084-5.55070.3041160.29632459X-RAY DIFFRACTION93
5.5507-35.71720.26261320.24352618X-RAY DIFFRACTION95

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