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Yorodumi- PDB-4wid: Crystal structure of the immediate-early 1 protein (IE1) at 2.31 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wid | |||||||||
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Title | Crystal structure of the immediate-early 1 protein (IE1) at 2.31 angstrom (tetragonal form after crystal dehydration) | |||||||||
Components | (RhUL123) x 2 | |||||||||
Keywords | VIRAL PROTEIN / Antagonist / cytomegalovirus | |||||||||
Function / homology | : / Cytomegalovirus IE1/IE2 / Cytomegalovirus IE1 protein / DNA-templated viral transcription / RhUL123 Function and homology information | |||||||||
Biological species | Macacine herpesvirus 3 (Rhesus cytomegalovirus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | |||||||||
Authors | Klingl, S. / Scherer, M. / Sevvana, M. / Muller, Y.A. / Stamminger, T. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: Plos Pathog. / Year: 2014 Title: Crystal Structure of Cytomegalovirus IE1 Protein Reveals Targeting of TRIM Family Member PML via Coiled-Coil Interactions. Authors: Scherer, M. / Klingl, S. / Sevvana, M. / Otto, V. / Schilling, E.M. / Stump, J.D. / Muller, R. / Reuter, N. / Sticht, H. / Muller, Y.A. / Stamminger, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wid.cif.gz | 300.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wid.ent.gz | 244.3 KB | Display | PDB format |
PDBx/mmJSON format | 4wid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wid_validation.pdf.gz | 465 KB | Display | wwPDB validaton report |
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Full document | 4wid_full_validation.pdf.gz | 472.6 KB | Display | |
Data in XML | 4wid_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 4wid_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/4wid ftp://data.pdbj.org/pub/pdb/validation_reports/wi/4wid | HTTPS FTP |
-Related structure data
Related structure data | 4w1cS 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: 42265.668 Da / Num. of mol.: 1 / Fragment: UNP residues 36-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macacine herpesvirus 3 (Rhesus cytomegalovirus) Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2FAE9 | ||
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#2: Protein | Mass: 42239.633 Da / Num. of mol.: 1 / Fragment: UNP residues 36-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macacine herpesvirus 3 (Rhesus cytomegalovirus) Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2FAE9 | ||
#3: Chemical | ChemComp-TRS / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Reservoir 700 microL: 15 % (w/v) PEG 3350, 400 mM magnesium formate, Drop ratio: 1 to 2 microL protein solution (20 mg/mL) plus 1 microL of reservoir solution supplemented with crystal microseeds PH range: approx. 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 17, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→48.18 Å / Num. obs: 37710 / % possible obs: 99.27 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.52 |
Reflection shell | Resolution: 2.306→2.389 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.56 / % possible all: 93.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Chain A of PDB 4W1C Resolution: 2.31→48.18 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 31.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→48.18 Å
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Refine LS restraints |
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LS refinement shell |
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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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