+Open data
-Basic information
Entry | Database: PDB / ID: 7w27 | ||||||
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Title | Crystal structure of BEND3-BEN4-DNA complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / protein-DNA interactions / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of ATP metabolic process / rDNA binding / rDNA heterochromatin formation / : / negative regulation of transcription by RNA polymerase I / heterochromatin / protein homooligomerization / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Zheng, L. / Ren, A. | ||||||
Funding support | China, 1items
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Citation | Journal: Genes Dev. / Year: 2022 Title: Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins. Authors: Zheng, L. / Liu, J. / Niu, L. / Kamran, M. / Yang, A.W.H. / Jolma, A. / Dai, Q. / Hughes, T.R. / Patel, D.J. / Zhang, L. / Prasanth, S.G. / Yu, Y. / Ren, A. / Lai, E.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w27.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w27.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 7w27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/7w27 ftp://data.pdbj.org/pub/pdb/validation_reports/w2/7w27 | HTTPS FTP |
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-Related structure data
Related structure data | 4ix7S 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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Unit cell |
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-Components
#1: DNA chain | Mass: 3946.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 4039.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Protein | Mass: 13196.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BEND3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5T5X7 |
#4: 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: 2.56 Å3/Da / Density % sol: 51.92 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / Details: 0.1 M BIS-TRIS, pH 6.5, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.49→50 Å / Num. obs: 35876 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 21.82 Å2 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.043 / Rrim(I) all: 0.137 / Χ2: 2.112 / Net I/σ(I): 5.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IX7 Resolution: 1.49→30.8 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.07 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.76 Å2 / Biso mean: 35.0134 Å2 / Biso min: 15.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.49→30.8 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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