+Open data
-Basic information
Entry | Database: PDB / ID: 4z9h | ||||||
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Title | Asp-Tar from E. coli | ||||||
Components | Methyl-accepting chemotaxis protein II | ||||||
Keywords | PROTEIN BINDING / Bacterial chemotaxis / Aspartate receptor | ||||||
Function / homology | Function and homology information detection of chemical stimulus / methyl accepting chemotaxis protein complex / protein histidine kinase binding / positive regulation of post-translational protein modification / cell tip / regulation of chemotaxis / signal complex assembly / cellular response to amino acid stimulus / protein homooligomerization / chemotaxis ...detection of chemical stimulus / methyl accepting chemotaxis protein complex / protein histidine kinase binding / positive regulation of post-translational protein modification / cell tip / regulation of chemotaxis / signal complex assembly / cellular response to amino acid stimulus / protein homooligomerization / chemotaxis / transmembrane signaling receptor activity / signal transduction / protein homodimerization activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.452 Å | ||||||
Authors | Mise, T. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Structural Analysis of the Ligand-Binding Domain of the Aspartate Receptor Tar from Escherichia coli Authors: Mise, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z9h.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z9h.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 4z9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/4z9h ftp://data.pdbj.org/pub/pdb/validation_reports/z9/4z9h | HTTPS FTP |
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-Related structure data
Related structure data | 4z9iC 4z9jC 2asrS 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: 22283.730 Da / Num. of mol.: 2 / Fragment: UNP residues 26-193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: tar, cheM / Production host: Escherichia coli (E. coli) / References: UniProt: P07017 #2: Chemical | ChemComp-ASP / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.46 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / Details: NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.452→24.57 Å / Num. obs: 65392 / % possible obs: 98.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.452→1.53 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.1 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ASR Resolution: 1.452→24.57 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.125 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 23.461 Å2
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Refinement step | Cycle: LAST / Resolution: 1.452→24.57 Å
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Refine LS restraints |
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