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- PDB-4yix: Structure of MRB1590 bound to ADP -

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Basic information

Entry
Database: PDB / ID: 4yix
TitleStructure of MRB1590 bound to ADP
ComponentsUncharacterized protein
KeywordsRNA BINDING PROTEIN / kRNA editing / MRB1590 / ATPase / RNA binding
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 / SAD / Resolution: 2.6 Å
AuthorsShaw, P.L.R. / Schumacher, 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 2, 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,50416
Polymers72,7971
Non-polymers2,70715
Water1,964109
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,00832
Polymers145,5942
Non-polymers5,41330
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area11110 Å2
ΔGint-626 kcal/mol
Surface area42160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.584, 184.709, 73.639
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-901-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 72797.234 Da / Num. of mol.: 1
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Hg
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: sodium/potassium tartrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→25.6 Å / Num. obs: 20596 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.315 / Net I/av σ(I): 33.375 / Net I/σ(I): 9.8 / Num. measured all: 692747
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.05-2.098.80.60336410.937100
2.09-2.129.20.49336130.934100
2.12-2.169.30.42936410.958100
2.16-2.219.40.35536480.956100
2.21-2.269.50.31236300.986100
2.26-2.319.50.27536440.984100
2.31-2.379.60.24236331.009100
2.37-2.439.50.21136701.028100
2.43-2.59.60.1936491.025100
2.5-2.589.60.15936501.053100
2.58-2.689.60.13736681.074100
2.68-2.789.60.12136481.109100
2.78-2.919.60.136521.165100
2.91-3.069.60.08336791.267100
3.06-3.259.60.07336851.41100
3.25-3.519.50.06636951.806100
3.51-3.869.40.06337072.383100
3.86-4.429.20.0637312.811100
4.42-5.569.40.04637671.963100
5.56-5090.0339131.37999.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→25.6 Å / FOM work R set: 0.8214 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.62 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 1987 9.65 %
Rwork0.2042 18609 -
obs0.2097 20596 91.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.9 Å2 / Biso mean: 25.05 Å2 / Biso min: 2.71 Å2
Refinement stepCycle: final / Resolution: 2.6→25.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4429 0 41 115 4585
Biso mean--27.01 21.08 -
Num. residues----579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074530
X-RAY DIFFRACTIONf_angle_d1.0176148
X-RAY DIFFRACTIONf_chiral_restr0.039710
X-RAY DIFFRACTIONf_plane_restr0.004806
X-RAY DIFFRACTIONf_dihedral_angle_d16.0031672
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.6650.28191150.2131053116874
2.665-2.73690.29131200.22661160128080
2.7369-2.81740.30261320.22011204133684
2.8174-2.90820.30571340.23051236137087
2.9082-3.0120.29311400.23041300144090
3.012-3.13240.28451380.22421316145491
3.1324-3.27470.30171470.21681315146293
3.2747-3.44690.27431410.21241391153295
3.4469-3.66230.271470.20841418156597
3.6623-3.94410.25381470.18381432157998
3.9441-4.33930.18761530.17071420157398
4.3393-4.96330.21131560.1731444160098
4.9633-6.23820.2841500.20121434158496
6.2382-25.60090.2631670.221486165396

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