[English] 日本語
Yorodumi- PDB-1kd8: X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kd8 | ||||||
---|---|---|---|---|---|---|---|
Title | X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12Ia16V BASE-d12La16L | ||||||
Components |
| ||||||
Keywords | DE NOVO PROTEIN / coiled coil heterodimer | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Keating, A.E. / Malashkevich, V.N. / Tidor, B. / Kim, P.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kd8.cif.gz | 57 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kd8.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kd8_validation.pdf.gz | 467.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1kd8_full_validation.pdf.gz | 470.8 KB | Display | |
Data in XML | 1kd8_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 1kd8_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/1kd8 ftp://data.pdbj.org/pub/pdb/validation_reports/kd/1kd8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | The assembly is a dimer. There are three copies of the dimer intact in the asymmetric unit. |
-Components
#1: Protein/peptide | Mass: 4142.462 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 56.1 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9763 Å |
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: 1.85→35 Å / Num. all: 25471 / Num. obs: 25471 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.413 / % possible all: 99 |
Reflection | *PLUS Rmerge(I) obs: 0.06 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: calculated structure Resolution: 1.9→28.97 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: flat model / Bsol: 62.63 Å2 / ksol: 0.386808 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→28.97 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor obs: 0.232 / Rfactor Rfree: 0.276 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.8 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.328 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.263 |