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- PDB-6e4o: Structure of apo T. brucei RRM: P4(1)2(1)2 form -

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Basic information

Entry
Database: PDB / ID: 6e4o
TitleStructure of apo T. brucei RRM: P4(1)2(1)2 form
ComponentsRNA-binding protein, putative
KeywordsRNA BINDING PROTEIN / RRM / RNA binding
Function / homology
Function and homology information


mitochondrial mRNA processing / mitochondrial mRNA editing complex / kinetoplast / cytoplasmic side of mitochondrial outer membrane / RNA processing / ribonucleoprotein complex / mRNA binding / mitochondrion / nucleus / cytoplasm
Similarity search - Function
: / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-binding protein, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSchumacher, M.A.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: The RRM of the kRNA-editing protein TbRGG2 uses multiple surfaces to bind and remodel RNA.
Authors: Travis, B. / Shaw, P.L.R. / Liu, B. / Ravindra, K. / Iliff, H. / Al-Hashimi, H.M. / Schumacher, M.A.
History
DepositionJul 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein, putative
B: RNA-binding protein, putative
C: RNA-binding protein, putative
D: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)31,1954
Polymers31,1954
Non-polymers00
Water5,873326
1
A: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)7,7991
Polymers7,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)7,7991
Polymers7,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)7,7991
Polymers7,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)7,7991
Polymers7,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.100, 72.100, 118.724
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-332-

HOH

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Components

#1: Protein
RNA-binding protein, putative


Mass: 7798.736 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q389P7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.2-1.4 M trisodium citrate, HEPES buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→38.676 Å / Num. obs: 28420 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / CC1/2: 0.997 / Rpim(I) all: 0.035 / Rsym value: 0.05 / Net I/σ(I): 12.5
Reflection shellResolution: 1.8→1.97 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2.3 / CC1/2: 0.977 / Rpim(I) all: 0.208 / Rsym value: 0.212 / % possible all: 80.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E4N

6e4n


Resolution: 1.8→38.676 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.34
RfactorNum. reflection% reflection
Rfree0.1968 2000 7.04 %
Rwork0.1651 --
obs0.1674 28420 95.52 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 40.113 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 89.64 Å2 / Biso mean: 23.49 Å2 / Biso min: 6.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.4723 Å20 Å2-0 Å2
2--2.4723 Å20 Å2
3----4.9445 Å2
Refinement stepCycle: final / Resolution: 1.8→38.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 0 326 2493
Biso mean---33.75 -
Num. residues----280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062202
X-RAY DIFFRACTIONf_angle_d0.892977
X-RAY DIFFRACTIONf_chiral_restr0.059346
X-RAY DIFFRACTIONf_plane_restr0.003386
X-RAY DIFFRACTIONf_dihedral_angle_d15.706784
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.86430.26311530.25672032218576
1.8643-1.9390.26091860.20472450263690
1.939-2.02720.20652000.17282634283497
2.0272-2.13410.18722060.16132724293099
2.1341-2.26780.21122060.153627262932100
2.2678-2.44290.21452070.164227342941100
2.4429-2.68870.21562080.170927452953100
2.6887-3.07760.21512080.17052757296599
3.0776-3.87680.17052100.14332764297498
3.8768-38.68520.16742160.16212854307096
Refinement TLS params.Method: refined / Origin x: 23.5625 Å / Origin y: -4.4708 Å / Origin z: -0.5355 Å
111213212223313233
T0.1144 Å2-0.0089 Å2-0.0154 Å2-0.0458 Å2-0.0138 Å2--0.0771 Å2
L0.2821 °2-0.1637 °20.1095 °2-0.3753 °2-0.5917 °2--1.0439 °2
S0.0253 Å °0.0215 Å °-0.0088 Å °-0.0877 Å °0.0234 Å °0.0189 Å °0.2414 Å °-0.0016 Å °0.0771 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA199 - 269
2X-RAY DIFFRACTION1allB199 - 267
3X-RAY DIFFRACTION1allC202 - 267
4X-RAY DIFFRACTION1allD200 - 267
5X-RAY DIFFRACTION1allS1 - 326

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