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- PDB-2gia: Crystal structures of trypanosoma bruciei MRP1/MRP2 -

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Basic information

Entry
Database: PDB / ID: 2gia
TitleCrystal structures of trypanosoma bruciei MRP1/MRP2
Components
  • mitochondrial RNA-binding protein 1
  • mitochondrial RNA-binding protein 2
KeywordsTRANSLATION / T. brucei / guide RNA / matchmaking / RNA editing
Function / homology
Function and homology information


RNA modification / mRNA modification / kinetoplast / nuclear lumen / post-transcriptional regulation of gene expression / mRNA binding / regulation of DNA-templated transcription / mitochondrion / DNA binding / RNA binding
Similarity search - Function
Transcriptional Co-activator pc4; Chain A - #40 / SUN domain-containing protein 1, N-terminal / Mitochondrial RNA binding protein MRP / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / GBP21 / Guide RNA binding protein gBP25
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.89 Å
AuthorsSchumacher, M.A. / Karamooz, E. / Zikova, A. / Trantirek, L. / Lukes, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Crystal Structures of T. brucei MRP1/MRP2 Guide-RNA Binding Complex Reveal RNA Matchmaking Mechanism.
Authors: Schumacher, M.A. / Karamooz, E. / Zikova, A. / Trantirek, L. / Lukes, J.
History
DepositionMar 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mitochondrial RNA-binding protein 2
B: mitochondrial RNA-binding protein 1
D: mitochondrial RNA-binding protein 1
G: mitochondrial RNA-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3346
Polymers86,2144
Non-polymers1202
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-28 kcal/mol
Surface area31720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.270, 85.700, 86.860
Angle α, β, γ (deg.)90.00, 109.38, 90.00
Int Tables number4
Space group name H-MP1211
DetailsMRP1/MRP2 form a heterotetramer with pseudo C4 symmetry

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Components

#1: Protein mitochondrial RNA-binding protein 2 / MRP2 / guide RNA-binding protein


Mass: 21914.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: TREU927 / Gene: mrp1 / Plasmid: petduet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q952G2
#2: Protein mitochondrial RNA-binding protein 1 / MRP1


Mass: 21192.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: TREU927 / Gene: mrp2 / Plasmid: petduet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P90629
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: peg 4000, sodium acetate, ammonium acetate, glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.989 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2005 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 1.89→58.7 Å / Num. all: 64446 / Num. obs: 63446 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.9 Å2
Reflection shellResolution: 1.89→1.92 Å / % possible all: 80

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Processing

Software
NameVersionClassification
ADSCdata collection
SCALAdata scaling
SOLVEphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.89→47.38 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1439847.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 5784 9.1 %RANDOM
Rwork0.179 ---
all0.1791 63446 --
obs0.1791 63430 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.8409 Å2 / ksol: 0.359874 e/Å3
Displacement parametersBiso mean: 37.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å20 Å20.35 Å2
2---2.37 Å20 Å2
3----0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.89→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4933 0 8 568 5509
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.08
LS refinement shellResolution: 1.89→2.01 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 725 8.8 %
Rwork0.259 7498 -
obs--74.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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