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- PDB-6pl6: Structural coordination of polymerization and crosslinking by a p... -

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Basic information

Entry
Database: PDB / ID: 6pl6
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


lipid-linked peptidoglycan transporter activity / peptidoglycan glycosyltransferase / peptidoglycan L,D-transpeptidase activity / peptidoglycan glycosyltransferase activity / cell division site / penicillin binding / 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 / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase ...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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AIX / 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: 3.3 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,3124
Polymers106,9603
Non-polymers3511
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)118.440, 118.440, 265.800
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: 40553.844 Da / Num. of mol.: 1 / Mutation: D255A
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-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / 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
#4: Chemical ChemComp-AIX / (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 351.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N3O4S
Has protein modificationY

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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: 5.07 Å3/Da / Density % sol: 75.76 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.6
Details: Protein complex was reconstituted with monoolein. Crystals were grown in 100 mM MES pH 5.8-6.8, 100 mM Na2SO4, 10 mM SrCl2, 35-45% PEG 300
PH range: 5.8-6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.3→49.235 Å / Num. obs: 59327 / % possible obs: 99.8 % / Redundancy: 6.77 % / Biso Wilson estimate: 127.67 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.243 / Net I/σ(I): 5.86
Reflection shellResolution: 3.3→3.39 Å / Redundancy: 6.82 % / Mean I/σ(I) obs: 0.58 / Num. unique obs: 2411 / CC1/2: 0.33 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PL5

6pl5


Resolution: 3.3→49.235 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.46
RfactorNum. reflection% reflection
Rfree0.3076 3914 6.6 %
Rwork0.2745 --
obs0.2769 59327 94.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 299.95 Å2 / Biso mean: 157.009 Å2 / Biso min: 71.75 Å2
Refinement stepCycle: final / Resolution: 3.3→49.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6840 0 24 0 6864
Biso mean--168.98 --
Num. residues----924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3002-3.34040.4507810.41661239132061
3.3404-3.38270.43191140.38991601171575
3.3827-3.42720.44321070.38711711181881
3.4272-3.47410.40211350.38411799193485
3.4741-3.52370.41531310.36261909204093
3.5237-3.57630.39771420.37722016215896
3.5763-3.63220.43861460.35682015216196
3.6322-3.69170.35951470.36742081222898
3.6917-3.75530.36121350.36032003213898
3.7553-3.82360.36231590.34112112227198
3.8236-3.89710.41611350.34962018215398
3.8971-3.97660.35731420.32912074221698
3.9766-4.06310.34731550.31492024217997
4.0631-4.15750.32471350.28251994212995
4.1575-4.26140.3111400.2932071221198
4.2614-4.37660.30611530.28362079223299
4.3766-4.50530.31411480.27142023217199
4.5053-4.65060.29981430.25622067221099
4.6506-4.81670.28651510.23582056220799
4.8167-5.00940.3191420.24632091223398
5.0094-5.23710.25091470.25272037218498
5.2371-5.51290.31871440.28052012215697
5.5129-5.85780.3881520.28032058221098
5.8578-6.30920.29551370.2642093223099
6.3092-6.94250.27821460.25712074222099
6.9425-7.94350.29641520.24762051220399
7.9435-9.99420.23411470.20512053220098
9.9942-49.24010.26231480.2552052220098
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)
17.5446-2.7555-2.0648.16421.62260.6782-0.71121.07250.3196-0.1527-0.2362-1.44790.76440.84360.63380.71690.22830.05541.13260.12150.689520.557367.6199-43.6211
24.89141.0418-1.7272.81041.06241.3665-0.1083-0.48160.27781.03040.07090.5699-0.35160.3917-0.03611.2994-0.0523-0.18071.87710.17050.796825.229449.8502-47.7713
36.3951-2.80981.47618.12-1.21030.39131.09010.36310.36780.7203-1.8307-0.52721.1806-2.5750.76362.31090.1003-0.12853.5169-0.34621.184523.978243.7067-34.0714
42.88390.8077-4.38342.7535-1.28938.0517-0.30920.2109-0.2678-0.60320.31960.37060.55020.22040.3292-0.04510.11260.80232.0450.3598-0.270910.214742.989-56.4565
54.01450.0618-4.58883.32662.97448.0814-0.6741-1.49051.36361.4369-0.0478-0.2214-0.21660.39930.73611.25140.1522-0.20351.1589-0.1260.87318.83737.8675-46.7247
65.8695-1.7252-3.06977.5127-2.42418.0022-0.3419-0.2071-0.2746-1.10280.3970.61770.5785-1.9307-0.28431.24430.0542-0.10772.03420.00760.16813.504547.6967-51.1452
73.73980.34482.12830.0691-0.80797.65031.0199-1.4799-0.06241.46310.23690.91623.4232-0.4691-0.93332.5401-0.4527-0.06271.2143-0.23050.7759-6.132442.1306-35.4217
83.2979-1.2552-2.41565.8041.68726.40580.32520.58130.288-0.72710.04510.3998-0.34471.7505-0.30131.0535-0.2920.09841.68880.06030.45178.366961.5271-39.3605
93.8461-0.38214.36873.15360.49985.2631.70461.0039-0.41740.7769-2.22910.04590.0040.52310.53211.5826-0.1044-0.12732.0050.0950.706311.995656.5086-35.6263
100.88162.46560.53247.40321.61650.35321.08992.266-1.137-0.3370.8608-0.42150.49450.9889-1.02181.21850.14210.02932.1531-0.34240.55420.355757.8546-57.0273
111.7368-0.4055-0.74611.4792-1.39336.77050.587-0.24410.84170.67390.26880.263-1.41990.4586-0.81061.3848-0.32210.09971.4396-0.02280.6892-1.837765.142-29.2933
121.7776-1.32060.85172.49431.16843.2634-0.3215-0.22280.3699-0.4870.6314-0.9456-0.00420.9593-0.5851.8742-0.27020.39611.898-0.03120.6144-6.32256.486512.3636
133.94380.03572.02054.73435.62397.5405-0.50421.5361.00680.32571.1141-0.70710.3326-0.5855-0.61671.35150.005-0.02531.20910.0310.8147-5.444760.01149.9258
145.3084-1.2644-0.23121.97110.50510.08040.66251.86750.5816-0.55970.1008-0.72090.8143-0.1238-0.68881.8876-0.3781-0.19332.30540.12340.9775-12.678739.979-5.6241
151.54191.91190.60711.60020.77760.371-0.0361-0.7127-0.07640.2968-0.0644-0.00620.0440.66890.04951.8744-0.4942-0.03581.96860.02030.7697-17.148145.9549-0.5469
163.46171.11610.38770.92320.10073.02550.0214-0.3011-0.45860.10520.13690.00781.0766-0.0629-0.15612.186-0.3218-0.0131.25030.06060.6354-35.885518.7904-0.9251
172.3012-1.58411.80621.3559-0.59943.026-0.3526-0.0978-0.554-0.3917-0.3422-0.97830.03780.21820.21030.3593-1.08270.4912-0.25930.60320.2103-9.621159.9116-1.5915
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 86 )A37 - 86
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 105 )A87 - 105
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 131 )A106 - 131
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 152 )A132 - 152
6X-RAY DIFFRACTION6chain 'A' and (resid 153 through 173 )A153 - 173
7X-RAY DIFFRACTION7chain 'A' and (resid 174 through 212 )A174 - 212
8X-RAY DIFFRACTION8chain 'A' and (resid 213 through 319 )A213 - 319
9X-RAY DIFFRACTION9chain 'A' and (resid 320 through 337 )A320 - 337
10X-RAY DIFFRACTION10chain 'A' and (resid 338 through 359 )A338 - 359
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 54 )B1 - 54
12X-RAY DIFFRACTION12chain 'B' and (resid 55 through 100 )B55 - 100
13X-RAY DIFFRACTION13chain 'B' and (resid 101 through 134 )B101 - 134
14X-RAY DIFFRACTION14chain 'B' and (resid 135 through 178 )B135 - 178
15X-RAY DIFFRACTION15chain 'B' and (resid 179 through 240 )B179 - 240
16X-RAY DIFFRACTION16chain 'B' and (resid 241 through 580 )B241 - 580
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 11 )D1 - 11

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