+Open data
-Basic information
Entry | Database: PDB / ID: 3d3k | ||||||
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Title | Crystal structure of human Edc3p | ||||||
Components | Enhancer of mRNA-decapping protein 3 | ||||||
Keywords | PROTEIN BINDING / hEdc3 / Phosphoprotein | ||||||
Function / homology | Function and homology information deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / P-body assembly / P-body / cytoplasmic ribonucleoprotein granule / mRNA binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Ling, S.H.M. | ||||||
Citation | Journal: Mol.Cell.Biol. / Year: 2008 Title: Crystal structure of human Edc3 and its functional implications Authors: Ling, S.H.M. / Decker, C.J. / Walsh, M.A. / She, M. / Parker, R. / Song, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d3k.cif.gz | 189.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d3k.ent.gz | 153.7 KB | Display | PDB format |
PDBx/mmJSON format | 3d3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d3k_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 3d3k_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 3d3k_validation.xml.gz | 36.7 KB | Display | |
Data in CIF | 3d3k_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/3d3k ftp://data.pdbj.org/pub/pdb/validation_reports/d3/3d3k | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 4 / Auth seq-ID: 258 - 506 / Label seq-ID: 9 - 257
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-Components
#1: Protein | Mass: 28587.133 Da / Num. of mol.: 4 / Fragment: C-terminal, UNP residues 250-508 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EDC3 / Plasmid: pGEX6p1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96F86 #2: Water | ChemComp-HOH / | |
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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: 2.86 Å3/Da / Density % sol: 56.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 6000, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9798 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å / Num. all: 66636 / Num. obs: 63120 |
Reflection shell | Highest resolution: 2.2 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.267 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.357 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1796 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.2→2.256 Å / 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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