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- PDB-6pl5: Structural coordination of polymerization and crosslinking by a p... -

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Basic information

Entry
Database: PDB / ID: 6pl5
TitleStructural coordination of polymerization and crosslinking by a peptidoglycan synthase complex
Components
  • Penicillin-binding protein 2/cell division protein FtsI
  • Peptidoglycan glycosyltransferase RodA
  • Unknown peptide
KeywordsMEMBRANE PROTEIN / Peptidoglycan Glycosyltransferase / transmembrane protein / Shape Elongation Division and Sporulation / elongasome / Peptidoglycan transpeptidase
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / membrane / 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 / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Peptidoglycan glycosyltransferase RodA / Penicillin-binding protein 2/cell division protein FtsI
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsSjodt, M. / Rohs, P.D.A. / Erlandson, S.C. / Zheng, S. / Rudner, D.Z. / Bernhardt, T.G. / 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: Nat Microbiol / Year: 2020
Title: Structural coordination of polymerization and crosslinking by a SEDS-bPBP peptidoglycan synthase complex.
Authors: Sjodt, M. / Rohs, P.D.A. / Gilman, M.S.A. / Erlandson, S.C. / Zheng, S. / Green, A.G. / Brock, K.P. / Taguchi, A. / Kahne, D. / Walker, S. / Marks, D.S. / Rudner, D.Z. / Bernhardt, T.G. / Kruse, A.C.
History
DepositionJun 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 10, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan glycosyltransferase RodA
B: Penicillin-binding protein 2/cell division protein FtsI
D: Unknown peptide


Theoretical massNumber of molelcules
Total (without water)107,0043
Polymers107,0043
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.570, 119.570, 267.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Peptidoglycan glycosyltransferase RodA / PGT / Cell elongation protein RodA / Cell wall polymerase / Peptidoglycan polymerase / PG polymerase


Mass: 40597.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: rodA, TTHA1241 / Plasmid: pCOLA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: Q5SIX3, peptidoglycan glycosyltransferase
#2: Protein Penicillin-binding protein 2/cell division protein FtsI


Mass: 65452.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1191 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q5SJ23
#3: Protein/peptide Unknown peptide


Mass: 954.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43

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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: 5.2 Å3/Da / Density % sol: 76.37 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.4
Details: Protein complex was reconstituted with monoolein. Crystals were grown in 100 mM MES pH 5.8-6.5, 100 mM Li2SO4, 40-50% PEG 300
PH range: 5.8-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.5→44.766 Å / Num. obs: 50777 / % possible obs: 99.3 % / Redundancy: 6.11 % / Biso Wilson estimate: 155.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.159 / Net I/σ(I): 8.15
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 6.11 % / Mean I/σ(I) obs: 0.62 / Num. unique obs: 2071 / CC1/2: 0.334 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BAR,3LO7

6bar

3lo7


Resolution: 3.5→44.766 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.31
RfactorNum. reflection% reflection
Rfree0.3053 3380 6.66 %
Rwork0.2855 --
obs0.2869 50777 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 419.99 Å2 / Biso mean: 175.8364 Å2 / Biso min: 75.51 Å2
Refinement stepCycle: final / Resolution: 3.5→44.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6843 0 0 0 6843
Num. residues----924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4999-3.54990.41231230.39941638176179
3.5499-3.60290.43251180.39181795191384
3.6029-3.65920.35231330.37331840197389
3.6592-3.71910.37131430.35761961210493
3.7191-3.78320.40591300.35661929205995
3.7832-3.8520.41221530.37462056220995
3.852-3.9260.40161360.35551972210896
3.926-4.00610.35381480.34392026217496
4.0061-4.09320.38981420.34431999214196
4.0932-4.18830.36851420.33472019216196
4.1883-4.2930.34211520.32752013216596
4.293-4.40890.34841420.31762013215596
4.4089-4.53860.34071390.31072018215797
4.5386-4.68490.37061390.30041980211996
4.6849-4.85220.3241470.27911954210194
4.8522-5.04620.31271350.28092055219095
5.0462-5.27550.28461410.28911960210195
5.2755-5.55320.3961460.29652014216096
5.5532-5.90040.35411520.29042044219698
5.9004-6.35480.2681430.2892049219297
6.3548-6.99210.31431360.29552040217697
6.9921-7.99890.28361540.2572006216097
7.9989-10.05890.22641460.20372020216697
10.0589-44.76970.22971400.26171996213695
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)
12.4773-4.1274-2.41249.57624.99972.7628-0.50130.32530.49770.21580.274-2.02710.49932.7353-0.19861.0615-0.22140.14492.0742-0.03111.093420.608367.6948-43.766
22.33621.08970.09927.02671.80560.35330.1226-1.09380.39991.3913-0.660.5027-0.1690.83270.48331.0151-0.0592-0.07452.7255-0.12271.322724.878348.0814-43.8613
33.9281-0.4008-5.03026.7871-2.12588.319-0.10770.07970.28-0.75840.3409-0.80580.96282.1051-0.22310.97270.0714-0.03061.5862-0.06270.60747.710542.9209-51.8539
43.69990.022.29821.0569-0.49643.29091.6237-1.7337-0.97552.0014-1.46841.40146.2087-1.8344-0.2363.4382-0.61140.12431.9213-0.13161.3734-6.090742.0908-35.3975
54.1527-1.7681-1.93222.21833.16996.2741-0.0570.1643-1.1103-0.59970.11391.01780.25121.72880.27741.0008-0.00570.28921.9137-0.30891.13796.888760.5147-24.1485
63.49371.3747-1.63373.85022.49216.97980.87460.897-0.29390.1936-0.4229-0.44950.35860.3961-0.32271.2995-0.3648-0.03932.1983-0.02060.640212.097360.212-46.7842
70.3599-1.16341.009-0.61450.24934.048-0.1029-0.1780.17690.13390.32-0.0302-0.08170.4675-0.25291.8126-0.40810.14421.8366-0.02090.9622-9.074553.4181-4.1977
83.02580.81910.76431.15970.48562.64680.1112-0.3394-0.62520.31380.0891-0.12061.5031-0.2227-0.22552.6512-0.4938-0.01631.37260.10270.8765-35.905218.8065-0.9415
92.66882.59591.17435.815-1.30042.3269-0.56750.0221-0.35230.0187-0.4684-0.7702-0.27830.40030.27890.6846-0.62480.17911.07370.02190.5344-9.552860.0872-1.5713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 36 )A8 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 105 )A37 - 105
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 173 )A106 - 173
4X-RAY DIFFRACTION4chain 'A' and (resid 174 through 212 )A174 - 212
5X-RAY DIFFRACTION5chain 'A' and (resid 213 through 256 )A213 - 256
6X-RAY DIFFRACTION6chain 'A' and (resid 257 through 359 )A257 - 359
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 240 )B1 - 240
8X-RAY DIFFRACTION8chain 'B' and (resid 241 through 580 )B241 - 580
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 11 )D1 - 11

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