+Open data
-Basic information
Entry | Database: PDB / ID: 4bpl | ||||||
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Title | rice importin_alpha in complex with nucleoplasmin NLS | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / NUCLEAR IMPORT / NUCLEAR LOCALIZATION SIGNAL | ||||||
Function / homology | Function and homology information sperm DNA decondensation / histone chaperone activity / importin-alpha family protein binding / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / positive regulation of DNA replication / nucleosome binding / histone binding / chromatin remodeling ...sperm DNA decondensation / histone chaperone activity / importin-alpha family protein binding / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / positive regulation of DNA replication / nucleosome binding / histone binding / chromatin remodeling / nucleolus / perinuclear region of cytoplasm / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ORYZA SATIVA (Asian cultivated rice) XENOPUS (frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Chang, C.-W. / Counago, R.M. / Williams, S.J. / Kobe, B. | ||||||
Citation | Journal: Mol.Plant / Year: 2014 Title: Structural Basis of Interaction of Bipartite Nuclear Localization Signal from Agrobacterium Vird2 with Rice Importin-Alpha Authors: Chang, C.-W. / Williams, S.J. / Counago, R.M. / Kobe, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bpl.cif.gz | 183.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bpl.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 4bpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bpl_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 4bpl_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 4bpl_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 4bpl_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/4bpl ftp://data.pdbj.org/pub/pdb/validation_reports/bp/4bpl | HTTPS FTP |
-Related structure data
Related structure data | 4bqkC 4b8oS 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 |
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Unit cell |
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-Components
#1: Protein | Mass: 49240.801 Da / Num. of mol.: 1 / Fragment: RESIDUES 73-526 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ORYZA SATIVA (Asian cultivated rice) / Plasmid: PET30A_RIMPALPHA1A_DIBB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q71VM4 |
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#2: Protein/peptide | Mass: 2232.710 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) XENOPUS (frog) / Plasmid: PGEX2T-NUCLEOPLASMINNLS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05221*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.2 % / Description: NONE |
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Crystal grow | pH: 6.2 / Details: 0.1 M MES PH 6.2 AND 1.35 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9536 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.89 Å / Num. obs: 29058 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 14.5 % / Biso Wilson estimate: 44.22 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4B8O Resolution: 2.3→19.89 Å / Cor.coef. Fo:Fc: 0.9365 / Cor.coef. Fo:Fc free: 0.9193 / SU R Cruickshank DPI: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.183
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Displacement parameters | Biso mean: 48.97 Å2
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Refine analyze | Luzzati coordinate error obs: 0.321 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Total num. of bins used: 15
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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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