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Yorodumi- PDB-3t30: Human nucleoplasmin (Npm2): a histone chaperone in oocytes and ea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t30 | ||||||
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Title | Human nucleoplasmin (Npm2): a histone chaperone in oocytes and early embryos | ||||||
Components | Nucleoplasmin-2 | ||||||
Keywords | CHAPERONE / beta-barrel jelly roll topology / Histone chaperone / H2A-H2B dimer and H3-H4 tetramer / oocytes and early embryos | ||||||
Function / homology | Function and homology information chromatin => GO:0000785 / oocyte differentiation / positive regulation of meiotic nuclear division / chromatin => GO:0000785 / positive regulation of DNA metabolic process / regulation of exit from mitosis / positive regulation of catalytic activity / blastocyst development / single fertilization / positive regulation of DNA replication ...chromatin => GO:0000785 / oocyte differentiation / positive regulation of meiotic nuclear division / chromatin => GO:0000785 / positive regulation of DNA metabolic process / regulation of exit from mitosis / positive regulation of catalytic activity / blastocyst development / single fertilization / positive regulation of DNA replication / histone binding / chromatin remodeling / chromatin binding / nucleolus / enzyme binding / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Platonova, O. / Head, J.F. / Akey, C.W. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Crystal structure and function of human nucleoplasmin (npm2): a histone chaperone in oocytes and embryos. Authors: Platonova, O. / Akey, I.V. / Head, J.F. / Akey, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t30.cif.gz | 202.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t30.ent.gz | 162.3 KB | Display | PDB format |
PDBx/mmJSON format | 3t30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t30_validation.pdf.gz | 514.4 KB | Display | wwPDB validaton report |
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Full document | 3t30_full_validation.pdf.gz | 545.8 KB | Display | |
Data in XML | 3t30_validation.xml.gz | 44.8 KB | Display | |
Data in CIF | 3t30_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/3t30 ftp://data.pdbj.org/pub/pdb/validation_reports/t3/3t30 | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12394.425 Da / Num. of mol.: 10 / Fragment: NPM2 oligomerisation domain (UNP residues 14-122) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NPM2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86SE8 #2: Water | ChemComp-HOH / | |
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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: 2.25 Å3/Da / Density % sol: 45.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% v/v PEG 3350, 100 mM NaCl, 25 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 76 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 23, 2007 |
Radiation | Monochromator: Si (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40.5 Å / Num. all: 86348 / Num. obs: 86130 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4 / Num. unique all: 8621 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1K5J (Xenopus nucleoplasmin) Resolution: 1.9→40.46 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.738 Å2 / ksol: 0.347 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→40.46 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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