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

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Basic information

Entry
Database: PDB / ID: 6bas
TitleCrystal structure of Thermus thermophilus Rod shape determining protein RodA D255A mutant (Q5SIX3_THET8)
ComponentsPeptidoglycan glycosyltransferase 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
Peptidoglycan glycosyltransferase RodA
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.194 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 1.4Oct 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: Peptidoglycan glycosyltransferase RodA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6802
Polymers38,6451
Non-polymers351
Water1448
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 Peptidoglycan glycosyltransferase RodA / PGT / Cell elongation protein RodA / Cell wall polymerase / Peptidoglycan polymerase / PG polymerase


Mass: 38644.969 Da / Num. of mol.: 1 / Mutation: D255A
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: rodA, TTHA1241 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SIX3, peptidoglycan glycosyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 59.4 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: Reconstituted in 10:1 monoolein:cholesterol mix. Precipitant solution: 35-50% PEG 200, 100 mM NaCl, 100mM MgCl2, 0.1 M Tris pH 7.6-8.3
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: 1.0333 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 3.194→40.006 Å / Num. obs: 13756 / % possible obs: 99.6 % / Redundancy: 3.43 % / CC1/2: 0.996 / Rsym value: 0.171 / Net I/σ(I): 4.08
Reflection shellResolution: 3.2→3.38 Å / Redundancy: 3.35 % / Mean I/σ(I) obs: 0.44 / Num. unique obs: 1200 / CC1/2: 0.417 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2880: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BAR

6bar


Resolution: 3.194→40.006 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3024 1360 9.89 %
Rwork0.2768 --
obs0.2793 13756 91.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.194→40.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 1 8 2210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042255
X-RAY DIFFRACTIONf_angle_d0.7513084
X-RAY DIFFRACTIONf_dihedral_angle_d12.5111264
X-RAY DIFFRACTIONf_chiral_restr0.041379
X-RAY DIFFRACTIONf_plane_restr0.006374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1941-3.30830.4541800.4532788X-RAY DIFFRACTION59
3.3083-3.44060.40041310.42721152X-RAY DIFFRACTION86
3.4406-3.59710.39931280.39381280X-RAY DIFFRACTION93
3.5971-3.78660.36451440.36011324X-RAY DIFFRACTION98
3.7866-4.02370.38271460.31961324X-RAY DIFFRACTION96
4.0237-4.3340.3211550.29511306X-RAY DIFFRACTION97
4.334-4.76950.27441460.25731285X-RAY DIFFRACTION96
4.7695-5.45820.29551470.25281285X-RAY DIFFRACTION95
5.4582-6.87110.34521380.29381332X-RAY DIFFRACTION98
6.8711-40.00910.22821450.211320X-RAY DIFFRACTION97

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