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- PDB-1kd9: X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kd9 | ||||||
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Title | X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L BASE-d12La16L | ||||||
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![]() | DE NOVO PROTEIN / coiled coil heterodimer | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Keating, A.E. / Malashkevich, V.N. / Tidor, B. / Kim, P.S. | ||||||
![]() | ![]() Title: Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils. Authors: Keating, A.E. / Malashkevich, V.N. / Tidor, B. / Kim, P.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54 KB | Display | ![]() |
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PDB format | ![]() | 41.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.3 KB | Display | ![]() |
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Full document | ![]() | 465.1 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.8 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | The assembly is a dimer. There are three copies of the dimer intact in the asymmetric unit. |
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Components
#1: Protein/peptide | Mass: 4156.490 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. #2: Protein/peptide | Mass: 4157.150 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.982 Å3/Da / Density % sol: 57.2 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: PEG 4000, Na Hepes, 2-propanol, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
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: Oct 19, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2→35 Å / Num. all: 20141 / Num. obs: 20141 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.04 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.337 / % possible all: 99.4 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 35 Å / Rmerge(I) obs: 0.04 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: calculated structure Resolution: 2.1→10 Å / Rfactor Rfree error: 0.007 / 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: 91.0823 Å2 / ksol: 0.440279 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.242 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 58.2 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.1 Å / Rfactor Rfree: 0.374 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.309 |