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- PDB-1q87: 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: 1q87 | ||||||
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Title | Crystal structure of the C-domain of the T.vaginalis Inr binding protein, IBP39 (tetragonal form) | ||||||
![]() | 39 kDa initiator binding protein | ||||||
![]() | DNA BINDING PROTEIN / Initiator / Inr / Initiator binding protein / core promoter | ||||||
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 / metal ion binding / 39 kDa initiator binding protein![]() | ||||||
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 | ![]() | 89.1 KB | Display | ![]() |
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PDB format | ![]() | 68.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.3 KB | Display | ![]() |
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Full document | ![]() | 449.4 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pp7C ![]() 1pp8C ![]() 1q88SC ![]() 1q89C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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: 2.23 Å3/Da / Density % sol: 44.97 % | ||||||||||||||||||||||||||||||
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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: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 12, 2002 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→65 Å / Num. obs: 19164 / % possible obs: 91.6 % / Observed criterion σ(F): 11 / Observed criterion σ(I): 10.9 / Redundancy: 5.8 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.042 |
Reflection shell | Resolution: 2.32→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2 / % possible all: 91.6 |
Reflection | *PLUS Lowest resolution: 65 Å / Num. measured all: 111463 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1Q88, C-domain from the C2 monoclinic form Resolution: 2.32→65 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1778869.52 / 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: 59.8645 Å2 / ksol: 0.351692 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.32→65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.32→2.47 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.275 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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