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Yorodumi- PDB-5t7m: LIGAND BINDING DOMAIN OF PSEUDOMONAS AERUGINOSA PAO1 AMINO ACID C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t7m | ||||||
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Title | LIGAND BINDING DOMAIN OF PSEUDOMONAS AERUGINOSA PAO1 AMINO ACID CHEMORECEPTOR PCTA IN COMPLEX WITH L-TRP | ||||||
Components | Chemotaxis proteinChemotaxis | ||||||
Keywords | SIGNALING PROTEIN / CHEMOTACTIC TRANSDUCER | ||||||
Function / homology | Function and homology information amino acid binding / response to amino acid / chemotaxis / transmembrane signaling receptor activity / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Gavira, J.A. / Rico-Jimenez, M. / Ortega, A. / Conejero-Muriel, M. / Zhulin, I. / Krell, T. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Mbio / Year: 2020 Title: How Bacterial Chemoreceptors Evolve Novel Ligand Specificities Authors: Gavira, J.A. / Jimenez-Rico, M. / Pineda-Molina, E. / Krell, T. #1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2013 Title: Purification, crystallization and preliminary crystallographic analysis of the ligand-binding regions of the PctA and PctB chemoreceptors from Pseudomonas aeruginosa in complex with amino acids. Authors: Rico-Jimenez, M. / Munoz-Martinez, F. / Krell, T. / Gavira, J.A. / Pineda-Molina, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t7m.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t7m.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 5t7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/5t7m ftp://data.pdbj.org/pub/pdb/validation_reports/t7/5t7m | HTTPS FTP |
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-Related structure data
Related structure data | 5lt9C 5ltoC 5ltvC 5ltxC 5t65SC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29473.318 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 1-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: pctA_1, mcpB_2, AO946_32780, AOY09_01348, PAERUG_P32_London_17_VIM_2_10_11_00198 Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H0Z019, UniProt: G3XD24*PLUS #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Nonpolymer details | L-TRYPTOPHAN | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 66 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 4.6 Details: COUNTERDIFFUSION METHOD: 2.0 M SODIUM FORMATE, 0.1 M NA ACT pH 4.6 PH range: 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→58.225 Å / Num. obs: 32028 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 40.24 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.25→2.32 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / CC1/2: 0.791 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5T65 Resolution: 2.25→58.225 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→58.225 Å
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Refine LS restraints |
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LS refinement shell |
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