+Open data
-Basic information
Entry | Database: PDB / ID: 4i1k | ||||||
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Title | Crystal Structure of VRN1 (Residues 208-341) | ||||||
Components | B3 domain-containing transcription factor VRN1 | ||||||
Keywords | DNA BINDING PROTEIN / B3 domain beta-barrel | ||||||
Function / homology | Function and homology information vernalization response / regulation of flower development / transcription cis-regulatory region binding / DNA binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | King, G. / Chanson, A.H. / McCallum, E.J. / Ohme-Takagi, M. / Byriel, K. / Hill, J.M. / Martin, J.L. / Mylne, J.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: The Arabidopsis B3 Domain Protein VERNALIZATION1 (VRN1) Is Involved in Processes Essential for Development, with Structural and Mutational Studies Revealing Its DNA-binding Surface. Authors: King, G.J. / Chanson, A.H. / McCallum, E.J. / Ohme-Takagi, M. / Byriel, K. / Hill, J.M. / Martin, J.L. / Mylne, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i1k.cif.gz | 125.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i1k.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 4i1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/4i1k ftp://data.pdbj.org/pub/pdb/validation_reports/i1/4i1k | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17017.479 Da / Num. of mol.: 2 / Fragment: B3 domain (UNP residues 208-341) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VRN1, At3g18990, K13E13.10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8L3W1 #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 19 mg/mL protein in 10 mM HEPES, pH 7.0, 50 mM sodium chloride, 5 mM DTT + equal volume well solution (0.1 M MES, pH 6.0, 1.4 M sodium chloride, 10 mM manganese chloride), VAPOR DIFFUSION, ...Details: 19 mg/mL protein in 10 mM HEPES, pH 7.0, 50 mM sodium chloride, 5 mM DTT + equal volume well solution (0.1 M MES, pH 6.0, 1.4 M sodium chloride, 10 mM manganese chloride), VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 16, 2008 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.956 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 34680 / Num. obs: 34680 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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LS refinement shell | Resolution: 1.6→1.66 Å / Num. reflection obs: 3439 |