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- PDB-1q88: Crystal structure of the C-domain of the T.vaginalis Inr binding ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q88 | ||||||
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Title | Crystal structure of the C-domain of the T.vaginalis Inr binding protein, IBP39 (monoclinic form) | ||||||
![]() | 39 kDa initiator binding protein | ||||||
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Function / homology | Initiator binding domain / Initiator binding protein 39kDa, C-terminal / IBP39, C-terminal domain superfamily / Transcription-initiator DNA-binding domain IBD / Initiator binding protein 39 kDa / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Schumacher, M.A. / Johnson, P.J. | ||||||
![]() | ![]() Title: Structural Basis of Core Promoter Recognition in a Primitive Eukaryote Authors: Schumacher, M.A. / Lau, A.O.T. / Johnson, P.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.3 KB | Display | ![]() |
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PDB format | ![]() | 68.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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: 25727.221 Da / Num. of mol.: 2 / Fragment: C-domain, residues 127-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.49 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 5000, ammonium sulphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 10, 2000 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.42→49.7 Å / Num. obs: 18750 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 38.5 Å2 / Rsym value: 0.064 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.42→2.5 Å / % possible all: 83 |
Reflection | *PLUS Num. measured all: 62819 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.5 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.7036 Å2 / ksol: 0.343005 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.42→49.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.42→2.57 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 49.7 Å / % reflection Rfree: 5 % / Rfactor Rfree![]() ![]() | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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