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Yorodumi- PDB-6ncm: Crystal structure of the human FOXN3 DNA binding domain in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ncm | |||||||||
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Title | Crystal structure of the human FOXN3 DNA binding domain in complex with a forkhead-like (FHL) DNA sequence | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / sequence specific DNA binding / regulation of transcription DNA templated / DNA Binding Transcription Factor Activity / forkhead / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information craniofacial suture morphogenesis / : / mitotic G2 DNA damage checkpoint signaling / cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å | |||||||||
Authors | Rogers, J.M. / Jarrett, S.M. / Seegar, T.C. / Waters, C.T. / Hallworth, A.N. / Blacklow, S.C. / Bulyk, M.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Mol. Cell / Year: 2019 Title: Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes. Authors: Rogers, J.M. / Waters, C.T. / Seegar, T.C.M. / Jarrett, S.M. / Hallworth, A.N. / Blacklow, S.C. / Bulyk, M.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ncm.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ncm.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ncm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/6ncm ftp://data.pdbj.org/pub/pdb/validation_reports/nc/6ncm | HTTPS FTP |
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-Related structure data
Related structure data | 6nceSC 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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-Components
#1: Protein | Mass: 11677.499 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FOXN3, C14orf116, CHES1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00409 #2: DNA chain | | Mass: 4913.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 4882.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.34 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M BisTris pH 5.5, 0.2 M NaCl, 22% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.704→39.3 Å / Num. obs: 9108 / % possible obs: 99.16 % / Redundancy: 6.5 % / Biso Wilson estimate: 81.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09034 / Rpim(I) all: 0.03907 / Rrim(I) all: 0.09872 / Net I/σ(I): 11.66 |
Reflection shell | Resolution: 2.704→2.801 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.949 / Mean I/σ(I) obs: 0.85 / Num. unique obs: 873 / CC1/2: 0.34 / Rrim(I) all: 2.115 / % possible all: 98.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NCE Resolution: 2.704→39.3 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 34.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.704→39.3 Å
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Refine LS restraints |
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LS refinement shell |
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