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Yorodumi- PDB-2vtx: ACTIVATION OF NUCLEOPLASMIN, AN OLIGOMERIC HISTONE CHAPERONE, CHA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vtx | ||||||
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Title | ACTIVATION OF NUCLEOPLASMIN, AN OLIGOMERIC HISTONE CHAPERONE, CHALLENGES ITS STABILITY | ||||||
Components | (NPM-A PROTEIN) x 2 | ||||||
Keywords | NUCLEAR PROTEIN / NUCLEOPLASMIN / PHOSPHORYLATION / PROTEIN STABILITY / OLIGOMERIC PROTEIN | ||||||
Function / homology | Function and homology information sperm DNA decondensation / histone chaperone activity / importin-alpha family protein binding / nucleosome binding / positive regulation of DNA replication / histone binding / chromatin remodeling / nucleolus / RNA binding / nucleoplasm ...sperm DNA decondensation / histone chaperone activity / importin-alpha family protein binding / nucleosome binding / positive regulation of DNA replication / histone binding / chromatin remodeling / nucleolus / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | XENOPUS LAEVIS (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Taneva, S.G. / Munoz, I.G. / Franco, G. / Falces, J. / Arregi, I. / Muga, A. / Montoya, G. / Urbaneja, M.A. / Banuelos, S. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Activation of Nucleoplasmin, an Oligomeric Histone Chaperone, Challenges its Stability. Authors: Taneva, S.G. / Munoz, I.G. / Franco, G. / Falces, J. / Arregi, I. / Muga, A. / Montoya, G. / Urbaneja, M.A. / Banuelos, S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vtx.cif.gz | 193.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vtx.ent.gz | 154.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vtx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vtx_validation.pdf.gz | 519.5 KB | Display | wwPDB validaton report |
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Full document | 2vtx_full_validation.pdf.gz | 545.1 KB | Display | |
Data in XML | 2vtx_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 2vtx_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/2vtx ftp://data.pdbj.org/pub/pdb/validation_reports/vt/2vtx | HTTPS FTP |
-Related structure data
Related structure data | 1k5jS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13384.168 Da / Num. of mol.: 9 / Fragment: CORE DOMAIN, RESIDUES 1-120 Source method: isolated from a genetically manipulated source Details: RESIDUES 2,3,5,7,8,15,66,96 FROM THE WTCORE WERE MUTATED TO ASP Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6GQG6, UniProt: P05221*PLUS #2: Protein | | Mass: 13396.222 Da / Num. of mol.: 1 / Fragment: CORE DOMAIN, RESIDUES 1-120 Source method: isolated from a genetically manipulated source Details: RESIDUES 2,3,5,7,8,15,66,96 FROM THE WTCORE WERE MUTATED TO ASP Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6GQG6, UniProt: P05221*PLUS #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, SER 3 TO ASP ENGINEERED RESIDUE IN CHAIN A, THR 4 TO ASP ENGINEERED ...ENGINEERED | |
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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: 2.75 Å3/Da / Density % sol: 54.86 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 15 MG/ML PROTEIN, 100MM NAAC, 20MM CACL2, 30% MPD, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9198 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9198 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. obs: 57758 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 17.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K5J Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.483 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.428 / ESU R Free: 0.301 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
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Refine LS restraints |
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