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- PDB-1qgv: HUMAN SPLICEOSOMAL PROTEIN U5-15KD -

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Basic information

Entry
Database: PDB / ID: 1qgv
TitleHUMAN SPLICEOSOMAL PROTEIN U5-15KD
ComponentsSPLICEOSOMAL PROTEIN U5-15KD
KeywordsTRANSCRIPTION / 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
Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin-like protein 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsReuter, 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
DepositionMay 6, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPLICEOSOMAL PROTEIN U5-15KD


Theoretical massNumber of molelcules
Total (without water)16,8071
Polymers16,8071
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.225, 65.092, 36.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein SPLICEOSOMAL PROTEIN U5-15KD


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mg/mlprotein1drop
220 mMTris-HCl1drop
3120 mM1dropNaCl
42 mMdithiothreitol1drop
51 mMEDTA1drop
62 mMdithiothreitol1reservoir
70.02 %(w/v)sodium azide1reservoir
81 Mammonium sulfate1reservoir
9200 mMHEPES/NaOH1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 28054 / % possible obs: 95.2 % / Redundancy: 13.6 % / Rsym value: 0.029
Reflection shellResolution: 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

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
SHARPphasing
X-PLOR3.851refinement
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -4.57 %RANDOM
Rwork0.216 ---
obs-27623 94.4 %-
Displacement parametersBiso mean: 27.9 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 0 144 1194
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.839
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.761.5
X-RAY DIFFRACTIONx_mcangle_it3.872
X-RAY DIFFRACTIONx_scbond_it2.962
X-RAY DIFFRACTIONx_scangle_it4.892.5
LS refinement shellResolution: 1.4→1.46 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.307 138 3.84 %
Rwork0.324 2997 -
obs--87.3 %
Xplor fileSerial 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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.839

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