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Yorodumi- PDB-1kdd: X-ray structure of the coiled coil GCN4 ACID BASE HETERODIMER ACI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kdd | ||||||
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Title | X-ray structure of the coiled coil GCN4 ACID BASE HETERODIMER ACID-d12La16I BASE-d12La16L | ||||||
Components |
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Keywords | DE NOVO PROTEIN / coiled coil heterodimer | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kdd.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kdd.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/1kdd ftp://data.pdbj.org/pub/pdb/validation_reports/kd/1kdd | HTTPS FTP |
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-Related structure data
-Links
-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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Components on special symmetry positions |
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Details | The assembly is a dimer. There are three copies of the dimer intact in the asymmetric unit. |
-Components
#1: Protein/peptide | Mass: 4157.150 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. #2: Protein/peptide | Mass: 4156.490 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.939 Å3/Da / Density % sol: 56.5 % | ||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0093 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 19, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0093 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→35 Å / Num. all: 18925 / Num. obs: 18925 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.257 / % possible all: 96.3 |
Reflection | *PLUS Lowest resolution: 35 Å / Rmerge(I) obs: 0.06 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: calculated structure Resolution: 2.14→19.91 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: 52.247 Å2 / ksol: 0.341169 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.14→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.14→2.27 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 Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor obs: 0.252 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 59.1 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.354 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.309 |