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- PDB-4dni: Structure of Editosome protein -

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Basic information

Entry
Database: PDB / ID: 4dni
TitleStructure of Editosome protein
ComponentsFusion protein of RNA-editing complex proteins MP42 and MP18
KeywordsPROTEIN BINDING / RNA BINDING PROTEIN / KREPA3 / KREPA6 / Editosome / Protein/RNA binding
Function / homology
Function and homology information


RNA modification / RNA endonuclease activity, producing 5'-phosphomonoesters / mitochondrial mRNA editing complex / mRNA modification / kinetoplast / response to metal ion / single-stranded DNA binding / 3'-5'-RNA exonuclease activity / endonuclease activity / mitochondrion ...RNA modification / RNA endonuclease activity, producing 5'-phosphomonoesters / mitochondrial mRNA editing complex / mRNA modification / kinetoplast / response to metal ion / single-stranded DNA binding / 3'-5'-RNA exonuclease activity / endonuclease activity / mitochondrion / RNA binding / zinc ion binding / nucleus
Similarity search - Function
RNA editing complex, nuclease subunit MP42 / RNA editing complex, subunit MP18 / Single-strand binding protein family / Primosome PriB/single-strand DNA-binding / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Nucleic acid-binding proteins ...RNA editing complex, nuclease subunit MP42 / RNA editing complex, subunit MP18 / Single-strand binding protein family / Primosome PriB/single-strand DNA-binding / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Nucleic acid-binding proteins / Zinc finger C2H2-type / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
MP18 RNA editing complex protein / RNA-editing complex protein MP42
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
Trypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsPark, Y.-J. / Hol, W.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Explorations of linked editosome domains leading to the discovery of motifs defining conserved pockets in editosome OB-folds.
Authors: Park, Y.J. / Hol, W.G.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion protein of RNA-editing complex proteins MP42 and MP18


Theoretical massNumber of molelcules
Total (without water)28,8671
Polymers28,8671
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.733, 59.418, 100.755
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fusion protein of RNA-editing complex proteins MP42 and MP18


Mass: 28866.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote), (gene. exp.) Trypanosoma brucei brucei (eukaryote)
Gene: KREPA3, KREPA6 / Plasmid: pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95W13, UniProt: Q38B90
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.4 M Potassium sodium tartrate tetrahydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2011
Diffraction measurementDetails: 0.50 degrees, 10.0 sec, detector distance 449.73 mm
Method: w scans
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionAv R equivalents: 0.1 / Number: 67051
ReflectionResolution: 2.55→50 Å / Num. obs: 11273 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 14.25
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.625 / Rsym value: 0.55 / % possible all: 70.7
Cell measurementReflection used: 67051

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→41.41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.2453 / WRfactor Rwork: 0.2137 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7928 / SU B: 10.899 / SU ML: 0.229 / SU R Cruickshank DPI: 0.5018 / SU Rfree: 0.2837 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.502 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 535 4.7 %RANDOM
Rwork0.214 ---
obs0.2157 11273 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.78 Å2 / Biso mean: 57.7999 Å2 / Biso min: 28.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.55→41.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 0 14 2041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022082
X-RAY DIFFRACTIONr_angle_refined_deg0.9811.9362834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5535256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.54624.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68515330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4341510
X-RAY DIFFRACTIONr_chiral_restr0.0620.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211613
LS refinement shellResolution: 2.55→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 28 -
Rwork0.366 516 -
all-544 -
obs--67 %

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