+Open data
-Basic information
Entry | Database: PDB / ID: 1qgv | ||||||
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Title | HUMAN SPLICEOSOMAL PROTEIN U5-15KD | ||||||
Components | SPLICEOSOMAL PROTEIN U5-15KD | ||||||
Keywords | TRANSCRIPTION / SPLICEOSOMAL PROTEIN / SNRNP / THIOREDOXIN | ||||||
Function / homology | Function and homology information RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / cell division ...RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / cell division / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å | ||||||
Authors | Reuter, K. / Nottrott, S. / Fabrizio, P. / Luehrmann, R. / Ficner, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Identification, characterization and crystal structure analysis of the human spliceosomal U5 snRNP-specific 15 kD protein. Authors: Reuter, K. / Nottrott, S. / Fabrizio, P. / Luhrmann, R. / Ficner, R. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Overproduction, purification, crystallization and preliminary x-ray diffraction studies of the human spliceosomal protein U5-15kD. Authors: Reuter, K. / Ficner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qgv.cif.gz | 41.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qgv.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qgv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qgv_validation.pdf.gz | 411.4 KB | Display | wwPDB validaton report |
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Full document | 1qgv_full_validation.pdf.gz | 416 KB | Display | |
Data in XML | 1qgv_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 1qgv_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/1qgv ftp://data.pdbj.org/pub/pdb/validation_reports/qg/1qgv | 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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Unit cell |
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-Components
#1: Protein | Mass: 16807.346 Da / Num. of mol.: 1 / Fragment: FULL-LENGTH Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA / Cellular location: NUCLEUS / Gene: U5-15KD / Plasmid: PXC35-15K / Cellular location (production host): CYTOPLASM / Gene (production host): U5-15KD / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106 / References: UniProt: P83876 |
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#2: 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: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 1.0 M AMMONIUM SULPHATE 0.2 M HEPES/NAOH, PH 7.6 AT 294 K, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 7.8 / PH range high: 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 28054 / % possible obs: 95.2 % / Redundancy: 13.6 % / Rsym value: 0.029 |
Reflection shell | Resolution: 1.4→1.43 Å / Rsym value: 0.265 / % possible all: 86.1 |
Reflection | *PLUS Num. measured all: 130566 / Rmerge(I) obs: 0.029 |
Reflection shell | *PLUS % possible obs: 86.1 % / Rmerge(I) obs: 0.265 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.4→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 27.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.46 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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