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- PDB-6bar: Crystal structure of Thermus thermophilus Rod shape determining p... -

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Basic information

Entry
Database: PDB / ID: 6bar
TitleCrystal structure of Thermus thermophilus Rod shape determining protein RodA (Q5SIX3_THET8)
ComponentsRod shape determining protein RodA
KeywordsTRANSFERASE / Peptidoglycan Glycosyltransferase / transmembrane protein / Shape Elogation Division and Sporulation / elongasome
Function / homology
Function and homology information


lipid-linked peptidoglycan transporter activity / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / cell division site / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / plasma membrane
Similarity search - Function
Probable peptidoglycan glycosyltransferase RodA/MrdB / Cell cycle, FtsW / RodA / SpoVE, conserved site / Cell cycle proteins ftsW / rodA / spoVE signature. / Probable peptidoglycan glycosyltransferase FtsW/RodA / Cell cycle protein
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Peptidoglycan glycosyltransferase RodA
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.908 Å
AuthorsSjodt, M. / Brock, K. / Dobihal, G. / Rohs, P.D.A. / Green, A.G. / Hopf, T.A. / Meeske, A.J. / Marks, D.S. / Bernhardt, T.G. / Rudner, D.Z. / 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: Nature / Year: 2018
Title: Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis.
Authors: Sjodt, M. / Brock, K. / Dobihal, G. / Rohs, P.D.A. / Green, A.G. / Hopf, T.A. / Meeske, A.J. / Srisuknimit, V. / Kahne, D. / Walker, S. / Marks, D.S. / Bernhardt, T.G. / Rudner, D.Z. / Kruse, A.C.
History
DepositionOct 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Rod shape determining protein RodA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4735
Polymers38,6891
Non-polymers7844
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.405, 80.012, 47.827
Angle α, β, γ (deg.)90.00, 91.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Rod shape determining protein RodA


Mass: 38688.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1241 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SIX3
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.2
Details: 41.5% PEG 200, 100 mM NaCL, 100 mM MgCl2*6H2O, 100 mM Tris pH 8.2
PH range: 7.6-8.3

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2017
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.908→40.006 Å / Num. obs: 18684 / % possible obs: 98.4 % / Redundancy: 3.02 % / CC1/2: 0.997 / Rsym value: 0.106 / Net I/σ(I): 6.69
Reflection shellResolution: 2.908→3.1 Å / Redundancy: 3.15 % / Mean I/σ(I) obs: 0.69 / Num. unique obs: 1605 / CC1/2: 0.458 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2880: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.908→40.006 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.95
RfactorNum. reflection% reflection
Rfree0.2736 1851 9.91 %
Rwork0.229 --
obs0.2335 18684 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 104.2 Å2
Refinement stepCycle: LAST / Resolution: 2.908→40.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 44 52 2325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052323
X-RAY DIFFRACTIONf_angle_d0.8253160
X-RAY DIFFRACTIONf_dihedral_angle_d15.3171310
X-RAY DIFFRACTIONf_chiral_restr0.041382
X-RAY DIFFRACTIONf_plane_restr0.005382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9077-2.98630.38131370.38791257X-RAY DIFFRACTION91
2.9863-3.07410.41831370.35851268X-RAY DIFFRACTION93
3.0741-3.17330.38871470.3371336X-RAY DIFFRACTION95
3.1733-3.28670.36461390.33641299X-RAY DIFFRACTION95
3.2867-3.41820.33281370.30381314X-RAY DIFFRACTION93
3.4182-3.57370.32211470.28441271X-RAY DIFFRACTION94
3.5737-3.7620.3191460.27131336X-RAY DIFFRACTION95
3.762-3.99750.34721370.24111347X-RAY DIFFRACTION96
3.9975-4.30580.27471600.21081273X-RAY DIFFRACTION94
4.3058-4.73850.24091410.19521247X-RAY DIFFRACTION92
4.7385-5.42270.22941430.19971285X-RAY DIFFRACTION92
5.4227-6.82650.30341460.24991319X-RAY DIFFRACTION95
6.8265-40.00980.19571340.17131281X-RAY DIFFRACTION92

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