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Yorodumi- PDB-3kot: Structure of the Citrobacter freundii effector binding domain con... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kot | ||||||
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Title | Structure of the Citrobacter freundii effector binding domain containing three amino acid substitutions: T103V, S221A and Y264F | ||||||
Components | HTH-type transcriptional activator ampR | ||||||
Keywords | TRANSCRIPTION / alpha-beta-sandwich / Activator / DNA-binding / Transcription regulation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Citrobacter freundii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Mark, B.L. / Balcewich, M.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Crystal Structure of the AmpR Effector Binding Domain Provides Insight into the Molecular Regulation of Inducible AmpC beta-Lactamase. Authors: Balcewich, M.D. / Reeve, T.M. / Orlikow, E.A. / Donald, L.J. / Vocadlo, D.J. / Mark, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kot.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kot.ent.gz | 41.5 KB | Display | PDB format |
PDBx/mmJSON format | 3kot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kot_validation.pdf.gz | 441 KB | Display | wwPDB validaton report |
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Full document | 3kot_full_validation.pdf.gz | 442.3 KB | Display | |
Data in XML | 3kot_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 3kot_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/3kot ftp://data.pdbj.org/pub/pdb/validation_reports/ko/3kot | HTTPS FTP |
-Related 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: 24648.271 Da / Num. of mol.: 1 / Fragment: UNP residues 83-291, Effector binding domain / Mutation: T103V, S221A, Y264F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: ampR / Plasmid: pET15a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) GOLD HTE / References: UniProt: P12529 | ||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 17% PEG 10,000 100mM MES pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→26.63 Å / Num. all: 30240 / Num. obs: 15779 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 1.92 % / Biso Wilson estimate: 23.82 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 13.89 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.95 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 5.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→26.629 Å / SU ML: 0.27 / σ(F): 0.05 / σ(I): 2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.942 Å2 / ksol: 0.386 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→26.629 Å
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Refine LS restraints |
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LS refinement shell |
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