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Yorodumi- PDB-5d5n: Crystal Structure of the Human Cytomegalovirus pUL50-pUL53 Complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d5n | ||||||
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Title | Crystal Structure of the Human Cytomegalovirus pUL50-pUL53 Complex | ||||||
Components |
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Keywords | VIRAL PROTEIN / Viral Nuclear Egress Complex | ||||||
Function / homology | Function and homology information host cell nuclear inner membrane / viral budding from nuclear membrane / viral tegument / viral transcription / viral life cycle / HCMV Late Events / HCMV Early Events / membrane => GO:0016020 / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Human cytomegalovirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.44 Å | ||||||
Authors | Walzer, S.A. / Egerer-Sieber, C. / Hohl, K. / Sevvana, M. / Muller, Y.A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Crystal Structure of the Human Cytomegalovirus pUL50-pUL53 Core Nuclear Egress Complex Provides Insight into a Unique Assembly Scaffold for Virus-Host Protein Interactions. Authors: Walzer, S.A. / Egerer-Sieber, C. / Sticht, H. / Sevvana, M. / Hohl, K. / Milbradt, J. / Muller, Y.A. / Marschall, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d5n.cif.gz | 172.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d5n.ent.gz | 137.5 KB | Display | PDB format |
PDBx/mmJSON format | 5d5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/5d5n ftp://data.pdbj.org/pub/pdb/validation_reports/d5/5d5n | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19607.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human cytomegalovirus / Strain: AD169 / Gene: UL50 / Plasmid: pE-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16791, UniProt: Q6SW81*PLUS |
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#2: Protein | Mass: 28410.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human cytomegalovirus / Strain: AD169 / Gene: UL53 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P16794, UniProt: F5HFZ4*PLUS |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Protein concentration: 10-13 mg/ml Protein buffer: 50 mM Tris/HCl pH 8.0, 150 mM NaCl, 2 mM TCEP Reservoir solution: 0.2 mM CaCl2, 20 % (w/v) PEG 3350 Ratio: 1:1 protein:reservoir solution |
-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: PSI PILATUS 6M / Detector: PIXEL / Date: May 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→50 Å / Num. obs: 20319 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 68.3 Å2 / Rsym value: 0.088 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.44→2.5 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.3 / Rsym value: 1.298 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.44→46.08 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.909 / SU B: 29.698 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.281 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.975 Å2
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Refinement step | Cycle: LAST / Resolution: 2.44→46.08 Å
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