+Open data
-Basic information
Entry | Database: PDB / ID: 6wm8 | ||||||
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Title | Proliferation-Associated protein 2G4 (PA2G4) | ||||||
Components | Proliferation-associated protein 2G4 | ||||||
Keywords | RNA BINDING PROTEIN / ErbB-3 receptor binding protein / RNA-binding protein / Tumour suppressor / Proliferation-Associated protein | ||||||
Function / homology | Function and homology information positive regulation of cell differentiation / rRNA processing / transcription corepressor activity / azurophil granule lumen / regulation of translation / nucleic acid binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / Neutrophil degranulation ...positive regulation of cell differentiation / rRNA processing / transcription corepressor activity / azurophil granule lumen / regulation of translation / nucleic acid binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / Neutrophil degranulation / nucleolus / negative regulation of apoptotic process / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Gorman, M.A. / Stevenson, B.W. / Parker, M.W. | ||||||
Citation | Journal: To Be Published Title: PA2G4: A Structural Perspective Authors: Gorman, M.A. / Stevenson, B.W. / Parker, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wm8.cif.gz | 423.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wm8.ent.gz | 351 KB | Display | PDB format |
PDBx/mmJSON format | 6wm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/6wm8 ftp://data.pdbj.org/pub/pdb/validation_reports/wm/6wm8 | HTTPS FTP |
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-Related structure data
Related structure data | 2q8kS 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: 41252.965 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PA2G4, EBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UQ80 #2: Chemical | ChemComp-SO4 / #3: 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: 4.45 Å3/Da / Density % sol: 72.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 2.4M Ammonium Sulphate 100 sodium citrate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.956 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2017 |
Radiation | Monochromator: 1,1,1 Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.956 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→48.92 Å / Num. obs: 66388 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 50.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.036 / Rrim(I) all: 0.133 / Χ2: 1.01 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.6→2.66 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.414 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4395 / CC1/2: 0.73 / Rpim(I) all: 0.389 / Rrim(I) all: 1.467 / Χ2: 1.03 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q8K Resolution: 2.6→48.92 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 17.821 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.232 / 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: 60.182 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→48.92 Å
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Refine LS restraints |
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