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Yorodumi- PDB-6pl5: Structural coordination of polymerization and crosslinking by a p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pl5 | ||||||
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Title | Structural coordination of polymerization and crosslinking by a peptidoglycan synthase complex | ||||||
Components |
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Keywords | MEMBRANE 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 glycosyltransferase activity / cell division site / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å | ||||||
Authors | Sjodt, M. / Rohs, P.D.A. / Erlandson, S.C. / Zheng, S. / Rudner, D.Z. / Bernhardt, T.G. / Kruse, A.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pl5.cif.gz | 371.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pl5.ent.gz | 303.5 KB | Display | PDB format |
PDBx/mmJSON format | 6pl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pl5_validation.pdf.gz | 445.6 KB | Display | wwPDB validaton report |
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Full document | 6pl5_full_validation.pdf.gz | 455 KB | Display | |
Data in XML | 6pl5_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 6pl5_validation.cif.gz | 43.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/6pl5 ftp://data.pdbj.org/pub/pdb/validation_reports/pl/6pl5 | HTTPS FTP |
-Related structure data
Related structure data | 6pl6C 3lo7S 6barS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 | 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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.2 Å3/Da / Density % sol: 76.37 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 419.99 Å2 / Biso mean: 175.8364 Å2 / Biso min: 75.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→44.766 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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