+Open data
-Basic information
Entry | Database: PDB / ID: 6y24 | ||||||
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Title | Crystal structure of fourth KH domain of FUBP1 | ||||||
Components | Far upstream element-binding protein 1 | ||||||
Keywords | RNA BINDING PROTEIN / KH4 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information single-stranded DNA binding / regulation of gene expression / mRNA binding / positive regulation of gene expression / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Ni, X. / Joerger, A.C. / Chaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Sci Rep / Year: 2020 Title: Comparative structural analyses and nucleotide-binding characterization of the four KH domains of FUBP1. Authors: Ni, X. / Knapp, S. / Chaikuad, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y24.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y24.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 6y24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/6y24 ftp://data.pdbj.org/pub/pdb/validation_reports/y2/6y24 | HTTPS FTP |
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-Related structure data
Related structure data | 6y2cC 6y2dC 4lijS 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: 10022.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FUBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96AE4 | ||||
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#2: Chemical | ChemComp-EDO / #3: 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: 2.23 Å3/Da / Density % sol: 44.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.1 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→55.04 Å / Num. obs: 7912 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.996 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.86→1.9 Å / Num. unique obs: 486 / CC1/2: 0.779 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LIJ Resolution: 1.86→35.02 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.907 / SU B: 7.983 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1339 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.136 Details: U VALUES : WITH TLS ADDED 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 | Biso max: 73.21 Å2 / Biso mean: 32.273 Å2 / Biso min: 18.38 Å2
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Refinement step | Cycle: final / Resolution: 1.86→35.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.908 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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