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- PDB-1kh0: Accurate Computer Base Design of a New Backbone Conformation in t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kh0 | ||||||
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Title | Accurate Computer Base Design of a New Backbone Conformation in the Second Turn of Protein L | ||||||
![]() | protein L | ||||||
![]() | PROTEIN BINDING / Protein L B1 domain / computational based protein design / Type 1' beta turn / extensive amino acid mutations. | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | O'Neill, J.W. / Kuhlman, B. / Kim, D.E. / Zhang, K.Y. / Baker, D. | ||||||
![]() | ![]() Title: Accurate computer-based design of a new backbone conformation in the second turn of protein L. Authors: Kuhlman, B. / O'Neill, J.W. / Kim, D.E. / Zhang, K.Y. / Baker, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.7 KB | Display | ![]() |
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PDB format | ![]() | 26 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.4 KB | Display | ![]() |
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Full document | ![]() | 435.5 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hz6S S: Starting model for refinement |
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Similar 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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Unit cell |
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Components
#1: Protein | Mass: 7124.085 Da / Num. of mol.: 2 / Fragment: B1 DOMAIN (RESIDUES 111-173) Mutation: F26K, T30L, A33V, Y34L, Y47W, V49I, A54T, D55N, K56G, G57B, Y58I, T59I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.74 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1M Sodium Citrate, 100mM Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 22, 2000 / Details: mirrors |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 11610 / Num. obs: 11610 / % possible obs: 96.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.043 / Net I/σ(I): 36.4 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 6.9 / Num. unique all: 923 / Rsym value: 0.252 / % possible all: 95.1 |
Reflection | *PLUS Lowest resolution: 25 Å |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HZ6 Resolution: 1.9→23.09 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1027037.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Maximum likelihood
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.2031 Å2 / ksol: 0.341182 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→23.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.265 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.208 |