+Open data
-Basic information
Entry | Database: PDB / ID: 2qx5 | ||||||
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Title | Structure of nucleoporin Nic96 | ||||||
Components | Nucleoporin NIC96 | ||||||
Keywords | TRANSPORT PROTEIN / nucleoporin / mRNA transport / Nuclear pore complex / Nucleus / Protein transport / Translocation / Transport | ||||||
Function / homology | Function and homology information nuclear pore linkers / nuclear pore organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport ...nuclear pore linkers / nuclear pore organization / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / ribosomal large subunit export from nucleus / nuclear pore / protein import into nucleus / nuclear envelope / nuclear membrane Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Jeudy, S. / Schwartz, T.U. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal structure of nucleoporin Nic96 reveals a novel, intricate helical domain architecture Authors: Jeudy, S. / Schwartz, T.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qx5.cif.gz | 459.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qx5.ent.gz | 375.4 KB | Display | PDB format |
PDBx/mmJSON format | 2qx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qx5_validation.pdf.gz | 445.6 KB | Display | wwPDB validaton report |
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Full document | 2qx5_full_validation.pdf.gz | 473.7 KB | Display | |
Data in XML | 2qx5_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 2qx5_validation.cif.gz | 58.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/2qx5 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/2qx5 | 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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Unit cell |
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-Components
#1: Protein | Mass: 75879.398 Da / Num. of mol.: 2 / Fragment: residues 186-839 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: NIC96 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P34077 #2: Chemical | #3: 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: 2.68 Å3/Da / Density % sol: 54.02 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 18% PEG 3350, 0.1M Bis Tris propane, 0.2M Potassium Thiocyanate, 1mM Cetyltrimethylammonium bromide, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0718 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0718 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 55385 / Num. obs: 55097 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 47.7 Å2 / Rsym value: 0.083 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.381 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.54 Å
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