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- PDB-4yj1: Crystal structure of T. brucei MRB1590-ADP bound to poly-U RNA -

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Basic information

Entry
Database: PDB / ID: 4yj1
TitleCrystal structure of T. brucei MRB1590-ADP bound to poly-U RNA
ComponentsUncharacterized protein
KeywordsRNA BINDING PROTEIN / kRNA editing / KASP / MRB1
Function / homology
Function and homology information


mitochondrial mRNA processing / mitochondrial RNA processing / cytidine to uridine editing / mRNA stabilization / nucleotide binding / mRNA binding / RNA binding / cytoplasm
Similarity search - Function
ATPase of the ABC class, N-terminal / ATPase of the ABC class, C-terminal / : / ATPase of the ABC class N-terminal / MRB1590 C-terminal domain / ABC transporter, ATPase, putative / P-loop domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Mitochondrial RNA binding complex 1 subunit
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSchumacher, M.A.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structures of the T. brucei kRNA editing factor MRB1590 reveal unique RNA-binding pore motif contained within an ABC-ATPase fold.
Authors: Shaw, P.L. / McAdams, N.M. / Hast, M.A. / Ammerman, M.L. / Read, L.K. / Schumacher, M.A.
History
DepositionMar 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5314
Polymers67,0551
Non-polymers4763
Water9,386521
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0628
Polymers134,1102
Non-polymers9526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area6370 Å2
ΔGint-68 kcal/mol
Surface area45160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.433, 215.433, 100.147
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-703-

MG

21A-804-

HOH

31A-881-

HOH

41A-908-

HOH

51A-915-

HOH

61A-917-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 67054.977 Da / Num. of mol.: 1 / Fragment: UNP residues 50-665
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb927.3.1590 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57ZF2
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 4.33 Å3/Da / Density % sol: 71.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, magnesium chloride

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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 315r / Detector: CCD / Date: Mar 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→41.8 Å / Num. obs: 70357 / % possible obs: 95.6 % / Redundancy: 4 % / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→41.8 Å / FOM work R set: 0.8779 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2029 3547 5.04 %
Rwork0.1734 66810 -
obs0.1748 70357 95.61 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.931 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 148 Å2 / Biso mean: 32.1 Å2 / Biso min: 11 Å2
Baniso -1Baniso -2Baniso -3
1--3.451 Å2-0 Å20 Å2
2---3.451 Å2-0 Å2
3---6.902 Å2
Refinement stepCycle: final / Resolution: 2.05→41.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4585 0 41 521 5147
Biso mean--46.88 39.98 -
Num. residues----600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024699
X-RAY DIFFRACTIONf_angle_d1.9056377
X-RAY DIFFRACTIONf_chiral_restr0.115730
X-RAY DIFFRACTIONf_plane_restr0.008840
X-RAY DIFFRACTIONf_dihedral_angle_d14.741738
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.12190.25793110.21976284659591
2.1219-2.20680.23193630.19626375673892
2.2068-2.30730.2183550.18196418677393
2.3073-2.42890.21963380.18116517685594
2.4289-2.58110.23183270.17676583691095
2.5811-2.78030.20813770.17626665704296
2.7803-3.060.20493820.1736754713697
3.06-3.50260.21463560.17966898725498
3.5026-4.41220.17893710.14987026739799
4.4122-41.85010.17953670.17172907657100

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