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Yorodumi- PDB-6un3: Crystal structure of Pseudomonas aeruginosa PBP3 in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6un3 | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa PBP3 in complex with ticarcillin | ||||||
Components | Peptidoglycan D,D-transpeptidase FtsI | ||||||
Keywords | HYDROLASE / temocillin / ticarcillin / pseudomonas aeruginosa PBP3 / penicillin-binding protein 3 / transpeptidase / HMM / high-molecular mass / b-lactam / lactam / penicillin | ||||||
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: 1.9 Å | ||||||
Authors | Sacco, M. / Chen, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: Antimicrob.Agents Chemother. / Year: 2019 Title: Influence of the alpha-Methoxy Group on the Reaction of Temocillin with Pseudomonas aeruginosa PBP3 and CTX-M-14 beta-Lactamase. Authors: Sacco, M.D. / Kroeck, K.G. / Kemp, M.T. / Zhang, X. / Andrews, L.D. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6un3.cif.gz | 121.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6un3.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 6un3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/6un3 ftp://data.pdbj.org/pub/pdb/validation_reports/un/6un3 | HTTPS FTP |
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-Related structure data
Related structure data | 6un1C 6unbC 3oc2S C: citing same article (ref.) 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: 57638.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: pbpB, ftsI, ftsI_1, ftsI_2, ALP65_00912, CAZ10_21230, CGU42_01090, DZ934_06595, DZ962_00565, E4V10_06485, EFK68_01815, IPC1492_18840, IPC3_13380, IPC605_16140, IPC669_10550, PAERUG_E15_London_ ...Gene: pbpB, ftsI, ftsI_1, ftsI_2, ALP65_00912, CAZ10_21230, CGU42_01090, DZ934_06595, DZ962_00565, E4V10_06485, EFK68_01815, IPC1492_18840, IPC3_13380, IPC605_16140, IPC669_10550, PAERUG_E15_London_28_01_14_00534, RW109_RW109_05757 Production host: Escherichia coli (E. coli) References: UniProt: Q51504, UniProt: G3XD46*PLUS, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-XT8 / ( |
#4: Chemical | ChemComp-CA / |
#5: 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: 2.22 Å3/Da / Density % sol: 44.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3350 0.2M CaOAc |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→60.872 Å / Num. all: 35128 / Num. obs: 35128 / % possible obs: 86.5 % / Redundancy: 5.3 % / Rpim(I) all: 0.057 / Rrim(I) all: 0.143 / Rsym value: 0.13 / Net I/av σ(I): 3.7 / Net I/σ(I): 6.5 / Num. measured all: 187384 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OC2 Resolution: 1.9→45.63 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.756 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.191 / 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: 94.26 Å2 / Biso mean: 33.111 Å2 / Biso min: 16.24 Å2
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Refinement step | Cycle: final / Resolution: 1.9→45.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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