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Yorodumi- PDB-7szy: High-resolution structure of the nuclease domain from the main re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7szy | ||||||
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Title | High-resolution structure of the nuclease domain from the main replication protein NS1 of Human Parvovirus B19 | ||||||
Components | NS1 protein | ||||||
Keywords | VIRAL PROTEIN / nuclease domain / viral origin of replication binding domain / parvovirus / double-stranded DNA binding / DNA nicking | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Human parvovirus B19 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Horton, N.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Virol. / Year: 2022 Title: High-Resolution Structure of the Nuclease Domain of the Human Parvovirus B19 Main Replication Protein NS1. Authors: Sanchez, J.L. / Ghadirian, N. / Horton, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7szy.cif.gz | 55.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7szy.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 7szy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/7szy ftp://data.pdbj.org/pub/pdb/validation_reports/sz/7szy | HTTPS FTP |
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-Related structure data
Related structure data | 7szxC 6usmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19884.779 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human parvovirus B19 / Production host: Escherichia coli (E. coli) / References: UniProt: A3F778 |
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#2: Chemical | ChemComp-CIT / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.03 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 15% PEG 3350 0.1M sodium citrate pH 4.5 0.1M NaCl 0.1M LiCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.06 Å / Num. obs: 6799 / % possible obs: 98.44 % / Redundancy: 2 % / Biso Wilson estimate: 28.31 Å2 / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.1022 / Rpim(I) all: 0.1022 / Rrim(I) all: 0.1446 / Net I/σ(I): 7.21 |
Reflection shell | Resolution: 2.4→2.486 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5331 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 665 / CC1/2: 0.385 / CC star: 0.745 / Rpim(I) all: 0.5331 / Rrim(I) all: 0.7539 / % possible all: 98.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6USM Resolution: 2.4→45.06 Å / SU ML: 0.2778 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1193 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.11 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→45.06 Å
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Refine LS restraints |
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LS refinement shell |
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