+Open data
-Basic information
Entry | Database: PDB / ID: 2ef8 | ||||||
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Title | Crystal structure of C.EcoT38IS | ||||||
Components | Putative transcription factor | ||||||
Keywords | TRANSCRIPTION REGULATOR / helix-turn-helix / DNA binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacteria phage P2 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 Å | ||||||
Authors | Kawanishi, Y. / Mikami, B. / Kita, K. | ||||||
Citation | Journal: To be published Title: Crystal structure of C.EcoT38IS Authors: Kawanishi, Y. / Mikami, B. / Kita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ef8.cif.gz | 45.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ef8.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ef8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ef8_validation.pdf.gz | 443.2 KB | Display | wwPDB validaton report |
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Full document | 2ef8_full_validation.pdf.gz | 446.1 KB | Display | |
Data in XML | 2ef8_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 2ef8_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/2ef8 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/2ef8 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9708.261 Da / Num. of mol.: 2 / Fragment: subunit A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage P2 (virus) / Genus: P2-like viruses / Strain: TH38 / Gene: ecoT38IC / Plasmid: pBSCEcoT38IS-Hisx6 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q83VS9 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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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: 2.37 Å3/Da / Density % sol: 48.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 2.0M Ammonium Sulfate, 0.1M Sodium Acetate trihydrate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 13, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→27.1 Å / Num. all: 13995 / Num. obs: 13953 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 9.5 / Num. unique all: 1381 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.95→14.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2712930.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.6166 Å2 / ksol: 0.404147 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→14.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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