+Open data
-Basic information
Entry | Database: PDB / ID: 3n89 | ||||||
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Title | KH domains | ||||||
Components | Defective in germ line development protein 3, isoform a | ||||||
Keywords | CELL CYCLE / KH domains / RNA binding / germline development | ||||||
Function / homology | Function and homology information germ-line sex determination / polynucleotide adenylyltransferase activator activity / masculinization of hermaphroditic germ-line / vulval development / germ-line stem cell division / nematode larval development / : / RNA-directed RNA polymerase complex / positive regulation of meiosis I / nuclear division ...germ-line sex determination / polynucleotide adenylyltransferase activator activity / masculinization of hermaphroditic germ-line / vulval development / germ-line stem cell division / nematode larval development / : / RNA-directed RNA polymerase complex / positive regulation of meiosis I / nuclear division / positive regulation of meiotic nuclear division / positive regulation of multicellular organism growth / cytosolic mRNA polyadenylation / P granule / embryo development ending in birth or egg hatching / RNA polymerase complex / mitotic cytokinesis / meiotic cell cycle / positive regulation of mitotic nuclear division / mRNA processing / regulation of translation / spermatogenesis / protein domain specific binding / positive regulation of gene expression / perinuclear region of cytoplasm / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.789 Å | ||||||
Authors | Nakel, K. / Hartung, S.A. / Bonneau, F. / Eckmann, C.R. / Conti, E. | ||||||
Citation | Journal: Rna / Year: 2010 Title: Four KH domains of the C. elegans Bicaudal-C ortholog GLD-3 form a globular structural platform. Authors: Nakel, K. / Hartung, S.A. / Bonneau, F. / Eckmann, C.R. / Conti, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n89.cif.gz | 143.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n89.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 3n89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n89_validation.pdf.gz | 439.9 KB | Display | wwPDB validaton report |
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Full document | 3n89_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 3n89_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 3n89_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/3n89 ftp://data.pdbj.org/pub/pdb/validation_reports/n8/3n89 | 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 42876.961 Da / Num. of mol.: 2 / Fragment: UNP residues 88-460 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: gld-3, T07F8.3 / Plasmid: pETM30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold pLyS / References: UniProt: Q95ZK7 #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: 3.48 Å3/Da / Density % sol: 64.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Ammoniumsulfate, Hepes, Glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.79→48.1 Å / Num. obs: 28664 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.134 / Net I/σ(I): 8.61 | ||||||||||||||||||
Reflection shell | Resolution: 2.79→3.07 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 7600 / Rsym value: 0.593 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.789→48.113 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 50.023 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.8 Å2 / Biso mean: 31.207 Å2 / Biso min: 10.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.789→48.113 Å
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Refine LS restraints |
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Xplor file |
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