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Open data
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Basic information
Entry | Database: PDB / ID: 5zkt | ||||||
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Title | Crystal structure of TCP domain of PCF6 in Oryza sativa | ||||||
![]() | Putative transcription factor PCF6 | ||||||
![]() | TRANSCRIPTION / TCP domain / OsPCF6 | ||||||
Function / homology | ![]() regulation of secondary shoot formation / sequence-specific DNA binding / DNA-binding transcription factor activity / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sun, L.F. / Zou, X.M. / Wu, Y.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of TCP domain of PCF6 in Oryza sativa Authors: Sun, L.F. / Zou, X.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35.2 KB | Display | ![]() |
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PDB format | ![]() | 22.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.3 KB | Display | ![]() |
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Full document | ![]() | 423.3 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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
#1: Protein | Mass: 6218.169 Da / Num. of mol.: 2 / Fragment: TCP domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: B1364A02.22, OJ1048_C10.23 / Plasmid: pET32a / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate pH4.6, 30% (w/v) PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.74→72.37 Å / Num. obs: 13997 / % possible obs: 98 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.016 / Rrim(I) all: 0.059 / Net I/σ(I): 27.7 / Num. measured all: 196470 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.93 Å2 / Biso mean: 32.5724 Å2 / Biso min: 17.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.74→37.415 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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