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Yorodumi- PDB-6usm: Structure of nuclease domain of human parvovirus B19 non-structur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6usm | ||||||
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Title | Structure of nuclease domain of human parvovirus B19 non-structural protein 1 in complex with zinc | ||||||
Components |
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Keywords | REPLICATION / B19 / DNA binding protein | ||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / viral genome replication ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / viral genome replication / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / nucleotide binding / DNA damage response / host cell nucleus / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Human parvovirus B19 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.37 Å | ||||||
Authors | Tewary, S.K. | ||||||
Citation | Journal: To Be Published Title: B19 Parvovirus Non-structural protein 1 in complex with zinc Authors: Tewary, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6usm.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6usm.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 6usm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6usm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6usm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6usm_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 6usm_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/6usm ftp://data.pdbj.org/pub/pdb/validation_reports/us/6usm | HTTPS FTP |
-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: 40805.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE / Production host: Expression vector pET-mod (others) / References: UniProt: C3SHQ8, UniProt: P0AEX9*PLUS |
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#2: Protein | Mass: 19475.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human parvovirus B19 / Gene: NS / Production host: Expression vector pET-mod (others) / References: UniProt: Q6TV13 |
#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#4: Chemical | ChemComp-ZN / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.2 M LiSo4 and sodium acetate tri-hydrate buffer of pH4.6 |
-Data collection
Diffraction | Mean temperature: 273 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.37→47.955 Å / Num. obs: 11564 / % possible obs: 96.8 % / Redundancy: 3 % / Biso Wilson estimate: 81.22 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.37→48 Å / Num. unique obs: 11564 / Rsym value: 0.125 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MBP Resolution: 3.37→47 Å / Cross valid method: THROUGHOUT /
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Displacement parameters | Biso mean: 88.23 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.37→47 Å
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Refine LS restraints |
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