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Yorodumi- PDB-7rd0: Crystal structure of C. difficile penicillin-binding protein 3 in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rd0 | |||||||||||||||
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Title | Crystal structure of C. difficile penicillin-binding protein 3 in apo form | |||||||||||||||
Components | Penicillin-binding protein | |||||||||||||||
Keywords | PEPTIDE BINDING PROTEIN / Peptidoglycan / PBP / PBP2 / cell wall / transpeptidase / b-lactam / gram-positive / spore / sporulation | |||||||||||||||
Function / homology | : Function and homology information | |||||||||||||||
Biological species | Clostridioides difficile (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||||||||
Authors | Sacco, M. / Chen, Y. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nat Commun / Year: 2022 Title: A unique class of Zn 2+ -binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile. Authors: Sacco, M.D. / Wang, S. / Adapa, S.R. / Zhang, X. / Lewandowski, E.M. / Gongora, M.V. / Keramisanou, D. / Atlas, Z.D. / Townsend, J.A. / Gatdula, J.R. / Morgan, R.T. / Hammond, L.R. / Marty, ...Authors: Sacco, M.D. / Wang, S. / Adapa, S.R. / Zhang, X. / Lewandowski, E.M. / Gongora, M.V. / Keramisanou, D. / Atlas, Z.D. / Townsend, J.A. / Gatdula, J.R. / Morgan, R.T. / Hammond, L.R. / Marty, M.T. / Wang, J. / Eswara, P.J. / Gelis, I. / Jiang, R.H.Y. / Sun, X. / Chen, Y. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rd0.cif.gz | 114.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rd0.ent.gz | 84.8 KB | Display | PDB format |
PDBx/mmJSON format | 7rd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rd0_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
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Full document | 7rd0_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 7rd0_validation.xml.gz | 19 KB | Display | |
Data in CIF | 7rd0_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/7rd0 ftp://data.pdbj.org/pub/pdb/validation_reports/rd/7rd0 | HTTPS FTP |
-Related structure data
Related structure data | 7rcwC 7rcxC 7rcyC 7rczC 5lp4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57840.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (strain R20291) (bacteria) Strain: R20291 / Gene: CDR20291_1067 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C9YKG6 | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15% PEG 4000, 0.2 M AmSO4, 0.1 M Na Citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 2, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→45.98 Å / Num. obs: 29788 / % possible obs: 99.9 % / Redundancy: 5.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.038 / Rrim(I) all: 0.093 / Net I/σ(I): 8.3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5lp4 Resolution: 2.4→45.98 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.046 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 160.36 Å2 / Biso mean: 59.413 Å2 / Biso min: 29.89 Å2
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Refinement step | Cycle: final / Resolution: 2.4→45.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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