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Open data
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Basic information
Entry | Database: PDB / ID: 3v1b | ||||||
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Title | Crystal structure of de novo designed MID1-apo2 | ||||||
![]() | Computational design, MID1-apo2 | ||||||
![]() | DE NOVO PROTEIN / METAL BINDING PROTEIN / Helix-turn-helix / metal binding / homodimer | ||||||
Function / homology | Rabenosyn, Rab binding domain / DNA Excision Repair, Uvrb; Chain A / Few Secondary Structures / Irregular![]() | ||||||
Biological species | ARTIFICIAL GENE (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Der, B.S. / Machius, M. / Miley, M.J. / Kuhlman, B. | ||||||
![]() | ![]() Title: Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. Authors: Der, B.S. / Machius, M. / Miley, M.J. / Mills, J.L. / Szyperski, T. / Kuhlman, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.5 KB | Display | ![]() |
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PDB format | ![]() | 55.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.7 KB | Display | ![]() |
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Full document | ![]() | 425.7 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v1aC ![]() 3v1cC ![]() 3v1dC ![]() 3v1eC ![]() 3v1fC ![]() 1yzmS S: Starting model for refinement C: citing same article ( |
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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/peptide | Mass: 5499.118 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARTIFICIAL GENE (others) / Plasmid: pQE-80L MBP fusion / Production host: ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.63 Å3/Da / Density % sol: 24.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 microliters protein (20 mg/ml, 100 mM ammonium acetate buffer) mixed with 0.1-0.2 microliters crystallization buffer (0.1 M MES, pH 6.0, 30% PEG 600, 5% PEG 1000, 10% glycerol), VAPOR ...Details: 0.1 microliters protein (20 mg/ml, 100 mM ammonium acetate buffer) mixed with 0.1-0.2 microliters crystallization buffer (0.1 M MES, pH 6.0, 30% PEG 600, 5% PEG 1000, 10% glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2010 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→21.7 Å / Num. all: 19067 / Num. obs: 19067 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 38.8 |
Reflection shell | Resolution: 1.28→1.29 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.5 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1YZM Resolution: 1.28→21.7 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
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Displacement parameters | Biso mean: 16.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.28→21.7 Å
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Refine LS restraints |
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LS refinement shell |
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