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- PDB-5d23: The crystal structure of STPR from Bombyx mori in complex with 13... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d23 | ||||||
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Title | The crystal structure of STPR from Bombyx mori in complex with 13-bp DNA derived from the +290 site of fibroin gene | ||||||
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![]() | TRANSCRIPTION/DNA / Protein-DNA complex / All a-helix / Major groove binding pattern / TRANSCRIPTION-DNA complex | ||||||
Function / homology | : / STPRs (score and three amino acid peptide repeats) / DNA / DNA (> 10) / Fibroin-modulator-binding protein-1![]() | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Cheng, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of an all-alpha protein running along the DNA major groove. Authors: Yu, L.Y. / Cheng, W. / Zhou, K. / Li, W.F. / Yu, H.M. / Gao, X. / Shen, X. / Wu, Q. / Chen, Y. / Zhou, C.Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.4 KB | Display | ![]() |
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PDB format | ![]() | 52.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.9 KB | Display | ![]() |
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Full document | ![]() | 426.6 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12047.971 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 99-193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: DNA chain | Mass: 7984.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 15% PEG4000, 20% 2-propanol, 0.1M sodium citrate pH5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 15446 / % possible obs: 98.2 % / Redundancy: 4.6 % / Net I/σ(I): 12.6 |
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Processing
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Refinement | Resolution: 1.95→27.45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.537 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.128 / 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: 47.583 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→27.45 Å
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Refine LS restraints |
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