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- PDB-3k81: Structure of the central interaction protein from the Trypanosoma... -

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Basic information

Entry
Database: PDB / ID: 3k81
TitleStructure of the central interaction protein from the Trypanosoma brucei editosome in complex with single domain antibodies
Components
  • MP18 RNA editing complex protein
  • Single strand antibody VHH domain
KeywordsImmune System / RNA Binding Protein / KREPA6 / VHH / Single domain antibody
Function / homology
Function and homology information


RNA modification / mitochondrial mRNA editing complex / kinetoplast / single-stranded DNA binding / endonuclease activity / RNA binding / nucleus
Similarity search - Function
RNA editing complex, subunit MP18 / Single-strand binding protein family / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
MP18 RNA editing complex protein
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsPark, Y.-J. / Hol, W.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Structures of a key interaction protein from the Trypanosoma brucei editosome in complex with single domain antibodies.
Authors: Wu, M. / Park, Y.J. / Pardon, E. / Turley, S. / Hayhurst, A. / Deng, J. / Steyaert, J. / Hol, W.G.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 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
C: MP18 RNA editing complex protein
D: MP18 RNA editing complex protein
A: Single strand antibody VHH domain
B: Single strand antibody VHH domain


Theoretical massNumber of molelcules
Total (without water)64,1624
Polymers64,1624
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.030, 68.605, 93.335
Angle α, β, γ (deg.)90.00, 102.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MP18 RNA editing complex protein


Mass: 18113.566 Da / Num. of mol.: 2 / Fragment: KREPA6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: KREPA6, Tb10.70.2090 / Plasmid: pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q38B90
#2: Antibody Single strand antibody VHH domain


Mass: 13967.477 Da / Num. of mol.: 2 / Fragment: single domain antibody VHH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 15% PEG3350, 0.1M Citrate pH.4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 1, 2009
Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 6402 / % possible obs: 92.3 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Biso Wilson estimate: 64.9 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 8.6
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2 / Num. unique all: 423 / Rsym value: 0.338 / % possible all: 61.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K7U

3k7u


Resolution: 3.4→33.467 Å / SU ML: 0.73 / σ(F): 1.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3198 301 4.73 %
Rwork0.2668 --
obs0.2693 6363 91.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 114.052 Å2 / ksol: 0.346 e/Å3
Refinement stepCycle: LAST / Resolution: 3.4→33.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 0 0 3250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023312
X-RAY DIFFRACTIONf_angle_d0.5444507
X-RAY DIFFRACTIONf_dihedral_angle_d13.0251110
X-RAY DIFFRACTIONf_chiral_restr0.038521
X-RAY DIFFRACTIONf_plane_restr0.002592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-4.28230.33871360.27472739X-RAY DIFFRACTION84
4.2823-33.46890.31061650.26273323X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 24.3208 Å / Origin y: 11.4461 Å / Origin z: -23.0129 Å
111213212223313233
T0.2762 Å20.0303 Å20.0143 Å2-0.0517 Å2-0.0428 Å2--0.1592 Å2
L1.1267 °2-0.5763 °2-0.0968 °2-0.6707 °2-1.2693 °2--1.9416 °2
S0.0604 Å °-0.143 Å °-0.1315 Å °-0.3351 Å °-0.0853 Å °0.0896 Å °0.0288 Å °0.1355 Å °-0.0547 Å °
Refinement TLS groupSelection details: all

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