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Yorodumi- PDB-8ik5: Transcription factor LMX1a homeobox domain in complex with Wnt1 p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ik5 | ||||||
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Title | Transcription factor LMX1a homeobox domain in complex with Wnt1 promoter | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / protein-dsDNA complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.989 Å | ||||||
Authors | Lv, M.Q. / Lin, L.Q. | ||||||
Funding support | China, 1items
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Citation | Journal: Febs J. / Year: 2024 Title: Structural insights into the recognition of the A/T-rich motif in target gene promoters by the LMX1a homeobox domain Authors: Lv, M.Q. / Lin, L.Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ik5.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ik5.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ik5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ik5_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
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Full document | 8ik5_full_validation.pdf.gz | 451.3 KB | Display | |
Data in XML | 8ik5_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 8ik5_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/8ik5 ftp://data.pdbj.org/pub/pdb/validation_reports/ik/8ik5 | HTTPS FTP |
-Related structure data
Related structure data | 8ikeC 8ilwC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4493.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
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#2: DNA chain | Mass: 4681.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
#3: Protein | Mass: 7981.499 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Sequence reference for homo sapiens is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A7K7QDL0. Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7K7QDL0 | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.85 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 27% PEG MME 2000, 0.1 mM sodium cacodylate (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.989→27.08 Å / Num. obs: 14659 / % possible obs: 99.08 % / Redundancy: 10.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.065 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 707 / CC1/2: 0.909 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.989→27.077 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.989→27.077 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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