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- PDB-2p87: Crystal structure of the C-terminal domain of C. elegans pre-mRNA... -

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Basic information

Entry
Database: PDB / ID: 2p87
TitleCrystal structure of the C-terminal domain of C. elegans pre-mRNA splicing factor Prp8
ComponentsPre-mRNA-splicing factor Prp8
KeywordsSPLICING / alpha-beta
Function / homology
Function and homology information


mRNA Splicing - Minor Pathway / mRNA Splicing - Major Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / catalytic step 2 spliceosome / metallopeptidase activity
Similarity search - Function
Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding ...Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Ribonuclease H-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pre-mRNA-splicing factor 8 homolog
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsZhang, L. / Shen, J. / Guarnieri, M.T. / Heroux, A. / Yang, K. / Zhao, R.
CitationJournal: Protein Sci. / Year: 2007
Title: Crystal structure of the C-terminal domain of splicing factor Prp8 carrying retinitis pigmentosa mutants
Authors: Zhang, L. / Shen, J. / Guarnieri, M.T. / Heroux, A. / Yang, K. / Zhao, R.
History
DepositionMar 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 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

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor Prp8


Theoretical massNumber of molelcules
Total (without water)31,1971
Polymers31,1971
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.063, 65.063, 135.552
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Pre-mRNA-splicing factor Prp8 / Prp8


Mass: 31197.045 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: prp-8 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P34369
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Hepes pH7, 14% PEK4K, 0.2M MgCl2, pH 7., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X26C11
SYNCHROTRONNSLS X26C20.9795
DetectorDetector: CCD / Date: May 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
ReflectionResolution: 2.3→50 Å / Num. all: 25097 / Num. obs: 23240 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2418 / % possible all: 96.2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1199 8.8 %random
Rwork0.226 ---
obs-12233 89.9 %-
Solvent computationBsol: 34.888 Å2
Displacement parametersBiso mean: 35.409 Å2
Baniso -1Baniso -2Baniso -3
1--2.476 Å20 Å20 Å2
2---2.476 Å20 Å2
3---4.953 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 0 121 2118
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.408
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param

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