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Yorodumi- PDB-5jvt: Crystal structure of the DNA binding domain of transcription fact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jvt | ||||||
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Title | Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with an 11-mer DNA GACCGGAAGTG | ||||||
Components |
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Keywords | transcription/dna / transcription / DNA binding / cancer / Ewing sarcoma / transcription-dna complex | ||||||
Function / homology | Function and homology information hemostasis / blood circulation / megakaryocyte development / Transcriptional regulation of granulopoiesis / animal organ morphogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body ...hemostasis / blood circulation / megakaryocyte development / Transcriptional regulation of granulopoiesis / animal organ morphogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / DNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Endothia gyrosa (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Hou, C. / Tsodikov, O.V. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: Structures of mithramycin analogues bound to DNA and implications for targeting transcription factor FLI1. Authors: Hou, C. / Weidenbach, S. / Cano, K.E. / Wang, Z. / Mitra, P. / Ivanov, D.N. / Rohr, J. / Tsodikov, O.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jvt.cif.gz | 206.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jvt.ent.gz | 162.1 KB | Display | PDB format |
PDBx/mmJSON format | 5jvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jvt_validation.pdf.gz | 480.5 KB | Display | wwPDB validaton report |
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Full document | 5jvt_full_validation.pdf.gz | 481.9 KB | Display | |
Data in XML | 5jvt_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 5jvt_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/5jvt ftp://data.pdbj.org/pub/pdb/validation_reports/jv/5jvt | HTTPS FTP |
-Related structure data
Related structure data | 5jvwC 5jw0C 5jw2C 5e8iS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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
-Protein , 1 types, 3 molecules ADG
#1: Protein | Mass: 12098.655 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FLI1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q01543 |
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-DNA chain , 2 types, 6 molecules BEHCFI
#2: DNA chain | Mass: 3423.248 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus) #3: DNA chain | Mass: 3285.148 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus) |
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-Non-polymers , 3 types, 4 molecules
#4: Chemical | ChemComp-PO4 / |
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#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.12 Å3/Da / Density % sol: 70.16 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.6 M ammonium sulphate, 0.1 M sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 17757 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5E8I Resolution: 3.1→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.933 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R: 0.814 / ESU R Free: 0.35 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: 1 / Resolution: 3.1→40 Å
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Refine LS restraints |
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