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Yorodumi- PDB-6hr9: Nitrocefin acylation of both catalytic serines of the Y409 mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hr9 | ||||||||||||
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Title | Nitrocefin acylation of both catalytic serines of the Y409 mutant of penicillin-binding protein 3 from P. aeruginosa | ||||||||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||||||||
Keywords | PENICILLIN-BINDING PROTEIN / peptidoglycan / HYDROLASE | ||||||||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||||||||
Authors | Bellini, D. / Dowson, C.G. | ||||||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Nitrocefin acylation of both catalytic serines of penicillin-binding protein 3 from P. aeruginosa Authors: Bellini, D. / Dowson, C.G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hr9.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hr9.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 6hr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hr9_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6hr9_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6hr9_validation.xml.gz | 21 KB | Display | |
Data in CIF | 6hr9_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/6hr9 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/6hr9 | HTTPS FTP |
-Related structure data
Related structure data | 3pboS S: Starting model for refinement |
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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: 57780.789 Da / Num. of mol.: 1 / Mutation: Y409 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: ftsI, pbpB, PA4418 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.37 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 25%(w/v) polyethylene glycol 3350, 0.1M Bis-Tris propane, 1%(w/v) protamine sulphate, pH 7.8. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→60.75 Å / Num. obs: 35268 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 46.48 Å2 / Rrim(I) all: 0.135 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.99→2.03 Å / Num. unique obs: 35268 / CC1/2: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PBO Resolution: 1.99→60.72 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.577 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.198 / 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: 138.48 Å2 / Biso mean: 40.911 Å2 / Biso min: 16.21 Å2
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Refinement step | Cycle: final / Resolution: 1.99→60.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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