+Open data
-Basic information
Entry | Database: PDB / ID: 6y2c | ||||||
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Title | Crystal structure of the third KH domain of FUBP1 | ||||||
Components | Far upstream element-binding protein 1 | ||||||
Keywords | RNA BINDING PROTEIN / ssDNA/RNA binding motif | ||||||
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: 2 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 | 6y2c.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y2c.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 6y2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/6y2c ftp://data.pdbj.org/pub/pdb/validation_reports/y2/6y2c | HTTPS FTP |
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-Related structure data
Related structure data | 6y24C 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 277 - 347 / Label seq-ID: 19 - 89
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-Components
#1: Protein | Mass: 10183.521 Da / Num. of mol.: 2 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 #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.36 Å3/Da / Density % sol: 47.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10% PEG 6000, 10% ethylene glycol, 0.015M Zinkchlorid, 0.1 M MES, pH 6.0 |
-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: 0.918 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: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2→41.1 Å / Num. obs: 13595 / % possible obs: 98.8 % / Redundancy: 4.5 % / CC1/2: 0.995 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2→2.05 Å / Num. unique obs: 999 / CC1/2: 0.661 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4lij Resolution: 2→41.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.41 / SU ML: 0.124 / SU R Cruickshank DPI: 0.1663 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.153 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: 75.46 Å2 / Biso mean: 35.66 Å2 / Biso min: 9.21 Å2
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Refinement step | Cycle: final / Resolution: 2→41.09 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1955 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2→2.052 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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