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Yorodumi- PDB-4ive: Crystal structure of a polyadenylate-binding protein 3 (PABPC3) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ive | ||||||
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Title | Crystal structure of a polyadenylate-binding protein 3 (PABPC3) from Homo sapiens at 2.30 A resolution | ||||||
Components | Polyadenylate-binding protein 3 | ||||||
Keywords | RNA BINDING PROTEIN / PABP unique domain / PF00658 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / RNA-BINDING PROTEIN / Partnership for T-Cell Biology / TCELL | ||||||
Function / homology | Function and homology information mRNA metabolic process / poly(A) binding / poly(U) RNA binding / mRNA 3'-UTR binding / cytoplasmic stress granule / ribonucleoprotein complex / extracellular exosome / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL) | ||||||
Citation | Journal: To be published Title: Crystal structure of a polyadenylate-binding protein 3 (PABPC3) from Homo sapiens at 2.30 A resolution Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ive.cif.gz | 134.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ive.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ive.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/4ive ftp://data.pdbj.org/pub/pdb/validation_reports/iv/4ive | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 10708.643 Da / Num. of mol.: 4 / Fragment: PABC domain residues 535-631 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BC027617, PABP3, PABPC3, PABPL3 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q9H361 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (535-631) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (535-631) WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.69 Å3/Da / Density % sol: 54.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.62 Details: 26.00% polyethylene glycol 6000, 0.1M MES pH 5.62, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979493,0.918401,0.979284 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2012 / Details: KOHZU: Double Crystal Si(111) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→43.128 Å / Num. obs: 20106 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.537 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.03 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→43.128 Å / Cor.coef. Fo:Fc: 0.9279 / Cor.coef. Fo:Fc free: 0.9277 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. CHLORIDE IONS MODELED ARE PRESENT IN CRYSTALLIZATION BUFFER. 3. A MET- ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. CHLORIDE IONS MODELED ARE PRESENT IN CRYSTALLIZATION BUFFER. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
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Displacement parameters | Biso max: 165.61 Å2 / Biso mean: 56.6623 Å2 / Biso min: 19.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.357 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→43.128 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.42 Å / Total num. of bins used: 10
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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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