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- PDB-1dvk: CRYSTAL STRUCTURE OF THE FUNCTIONAL DOMAIN OF THE SPLICING FACTOR... -

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Basic information

Entry
Database: PDB / ID: 1dvk
TitleCRYSTAL STRUCTURE OF THE FUNCTIONAL DOMAIN OF THE SPLICING FACTOR PRP18
ComponentsPRP18
KeywordsRNA BINDING PROTEIN / pre-mRNA Splicing factor / Prp18
Function / homology
Function and homology information


U2-type post-spliceosomal complex / nuclear mRNA surveillance / generation of catalytic spliceosome for second transesterification step / U5 snRNP / U4/U6 x U5 tri-snRNP complex / mRNA splicing, via spliceosome
Similarity search - Function
RNA Binding Protein, Prp18; Chain A / Functional domain of the splicing factor Prp18 / Prp18 / Pre-mRNA-splicing factor 18 / Prp18 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Pre-mRNA-splicing factor 18
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å
AuthorsJiang, J. / Horowitz, D.S. / Xu, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structure of the functional domain of the splicing factor Prp18.
Authors: Jiang, J. / Horowitz, D.S. / Xu, R.M.
History
DepositionJan 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRP18
B: PRP18


Theoretical massNumber of molelcules
Total (without water)39,2522
Polymers39,2522
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.935, 79.167, 171.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PRP18


Mass: 19625.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33411
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM MES 6.0, 25% PEG8000, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-10 mg/mlprotein1drop
2100 mMMES1reservoirpH6.0
310 %glycerol1reservoir
420 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.09
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 18919 / Num. obs: 17664 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 19.59 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.9
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.097 / % possible all: 55.7
Reflection
*PLUS
Num. measured all: 188477

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Processing

Software
NameClassification
PHASESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.15→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1759 -RANDOM
Rwork0.203 ---
all0.252 18919 --
obs0.203 17517 92.6 %-
Refinement stepCycle: LAST / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2427 0 0 219 2646
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d0.985
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg0.985
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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