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Yorodumi- PDB-5xsl: Crystal structure of the PWWP domain of human hepatoma-derived gr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xsl | ||||||
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Title | Crystal structure of the PWWP domain of human hepatoma-derived growth factor | ||||||
Components | Hepatoma-derived growth factor | ||||||
Keywords | HORMONE / Growth factor | ||||||
Function / homology | Function and homology information cellular response to interleukin-7 / positive regulation of cell division / protein localization to nucleus / transcription repressor complex / tubulin binding / transcription corepressor binding / growth factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / heparin binding ...cellular response to interleukin-7 / positive regulation of cell division / protein localization to nucleus / transcription repressor complex / tubulin binding / transcription corepressor binding / growth factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / heparin binding / negative regulation of neuron apoptotic process / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleotide binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Chen, L.Y. / Huang, Y.C. / Hsieh, Y.C. / Lin, P.J. / Chen, C.J. | ||||||
Citation | Journal: To Be Published Title: Structure of the PWWP domain at 3.3 Angstroms resolution Authors: Chen, L.Y. / Huang, Y.C. / Hsieh, Y.C. / Lin, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xsl.cif.gz | 32.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xsl.ent.gz | 19.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xsl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xsl_validation.pdf.gz | 428.6 KB | Display | wwPDB validaton report |
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Full document | 5xsl_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 5xsl_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 5xsl_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/5xsl ftp://data.pdbj.org/pub/pdb/validation_reports/xs/5xsl | HTTPS FTP |
-Related structure data
Related structure data | 3qbyS 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: Protein | Mass: 13735.487 Da / Num. of mol.: 1 / Fragment: UNP residues 1-100 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hdgf / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Codon plus-RIL / References: UniProt: Q8VHK7 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.75 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, Tris, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. obs: 3320 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.081 / Rsym value: 0.141 / Net I/σ(I): 21.89 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3.59 / CC1/2: 0.958 / Rsym value: 0.705 / Χ2: 0.94 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QBY Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.83 / SU B: 23.06 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R: 2.161 / ESU R Free: 0.477 / Details: 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 mean: 73.808 Å2
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Refinement step | Cycle: 1 / Resolution: 3.3→30 Å
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Refine LS restraints |
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