+Open data
-Basic information
Entry | Database: PDB / ID: 3v1c | ||||||
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Title | Crystal structure of de novo designed MID1-zinc | ||||||
Components | Computational design, MID1-zinc | ||||||
Keywords | DE NOVO PROTEIN / HYDROLASE / Helix-turn-helix / metal binding / homodimer / METAL BINDING PROTEIN | ||||||
Function / homology | Rabenosyn, Rab binding domain / DNA Excision Repair, Uvrb; Chain A / Few Secondary Structures / Irregular / L(+)-TARTARIC ACID / Unknown ligand Function and homology information | ||||||
Biological species | ARTIFICIAL GENE (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Phaser / Resolution: 1.129 Å | ||||||
Authors | Der, B.S. / Machius, M. / Miley, M.J. / Kuhlman, B. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v1c.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v1c.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 3v1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v1c_validation.pdf.gz | 454.7 KB | Display | wwPDB validaton report |
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Full document | 3v1c_full_validation.pdf.gz | 456.5 KB | Display | |
Data in XML | 3v1c_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 3v1c_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/3v1c ftp://data.pdbj.org/pub/pdb/validation_reports/v1/3v1c | HTTPS FTP |
-Related structure data
Related structure data | 3v1aC 3v1bC 3v1dC 3v1eC 3v1fC 1yzmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | In the crystal structure, the biological assembly (dimer) is located within the asymmetric unit. |
-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: Escherichia coli (E. coli) / Strain (production host): BL21 #2: Chemical | #3: Chemical | ChemComp-TLA / | #4: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #5: 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: 1.81 Å3/Da / Density % sol: 31.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1-2 microliter2 protein (20 mg/ml, 100 mM ammonium acetate buffer) mixed with 1 microliter crystallization buffer (0.1 M sodium citrate, pH 5.5, 1.25 M ammonium sulfate, 0.08 M K/Na tartrate) ...Details: 1-2 microliter2 protein (20 mg/ml, 100 mM ammonium acetate buffer) mixed with 1 microliter crystallization buffer (0.1 M sodium citrate, pH 5.5, 1.25 M ammonium sulfate, 0.08 M K/Na tartrate), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.918 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 26, 2011 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.129→19.292 Å / Num. all: 30296 / Num. obs: 30296 / % possible obs: 97.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 9.02 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 31.4 |
Reflection shell | Resolution: 1.13→1.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: Phaser Starting model: PDB ENTRY 1YZM Resolution: 1.129→19.292 Å / SU ML: 0.1 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.904 Å2 / ksol: 0.408 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.129→19.292 Å
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Refine LS restraints |
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LS refinement shell |
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