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Yorodumi- PDB-4uzc: KSHV LANA (ORF73) C-terminal domain, spiral: hexagonal crystal form -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uzc | ||||||
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Title | KSHV LANA (ORF73) C-terminal domain, spiral: hexagonal crystal form | ||||||
Components | ORF 73 | ||||||
Keywords | VIRAL PROTEIN / DNA-BINDING DOMAIN / ORIGIN-BINDING DOMAIN / OLIGOMERIZATION DOMAIN / HHV-8 / GAMMAHERPESVIRUS / RHADINOVIRUS / PRIMARY EFFUSION LYMPHOMA / MULTICENTRIC CASTLEMAN'S DISEASE / TUMOR VIRUS / CANCER | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host NF-kappaB cascade / viral life cycle / host cell nucleus / DNA binding Similarity search - Function | ||||||
Biological species | HUMAN HERPESVIRUS 8 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | ||||||
Authors | Hellert, J. / Krausze, J. / Luhrs, T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: The 3D Structure of Kaposi Sarcoma Herpesvirus Lana C-Terminal Domain Bound to DNA. Authors: Hellert, J. / Weidner-Glunde, M. / Krausze, J. / Lunsdorf, H. / Ritter, C. / Schulz, T.F. / Luhrs, T. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uzc.cif.gz | 116.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uzc.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 4uzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/4uzc ftp://data.pdbj.org/pub/pdb/validation_reports/uz/4uzc | HTTPS FTP |
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-Related structure data
Related structure data | 4uzbC 2ypyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 | x 11
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS IRREGULAR HELICAL SYMMETRY WITH THE FOLLOWING AVERAGE PARAMETERS: ROTATION PER DIMER (TWIST) = -75.00 DEGREES RISE PER DIMER (HEIGHT) = 9.51 ANGSTROMS |
-Components
#1: Protein | Mass: 15760.201 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, RESIDUES 1013-1149 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN HERPESVIRUS 8 / Plasmid: PET-BASED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76SB0, UniProt: Q9QR71*PLUS |
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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: 2.79 Å3/Da / Density % sol: 55.88 % Description: DATA IN RESOLUTION RANGE 3.93 A - 3.87 A IS EXCLUDED DUE TO THE PRESENCE OF AN ICE RING |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.4 UL OF 31.5 MG/ML PROTEIN IN 5 MM BISTRIS-CL, 5 MM DTT, PH 6.5 WERE AS SUCH EQUILIBRATED AGAINST A RESERVOIR SOLUTION OF 170 MM LITHIUM ACETATE AND 18% (W/V) PEG3350 IN A SITTING DROP ...Details: 0.4 UL OF 31.5 MG/ML PROTEIN IN 5 MM BISTRIS-CL, 5 MM DTT, PH 6.5 WERE AS SUCH EQUILIBRATED AGAINST A RESERVOIR SOLUTION OF 170 MM LITHIUM ACETATE AND 18% (W/V) PEG3350 IN A SITTING DROP SETUP AT 20 DEGREE CENTIGRADE. AFTER TWO DAYS, CRYSTALS WERE DETACHED FROM THE CARRIER PLASTIC BY ADDING 1 UL OF 2 M AMMONIUM FORMATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2014 / Details: MIRRORS |
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→89.36 Å / Num. obs: 7874 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 29.7 % / Biso Wilson estimate: 119.8 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 18.53 |
Reflection shell | Resolution: 3.7→3.84 Å / Redundancy: 31.3 % / Mean I/σ(I) obs: 1.92 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YPY Resolution: 3.7→89.36 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.908 / SU B: 40.346 / SU ML: 0.553 / Cross valid method: THROUGHOUT / ESU R Free: 0.692 / 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: 115.815 Å2
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Refinement step | Cycle: LAST / Resolution: 3.7→89.36 Å
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Refine LS restraints |
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