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- PDB-6p5r: Structure of T. brucei MERS1-GDP complex -

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Basic information

Entry
Database: PDB / ID: 6p5r
TitleStructure of T. brucei MERS1-GDP complex
ComponentsMitochondrial edited mRNA stability factor 1
KeywordsRNA BINDING PROTEIN / MERS1 / 5' end processing / mRNA
Function / homologyNUDIX domain / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / GUANOSINE-5'-DIPHOSPHATE / Mitochondrial edited mRNA stability factor 1
Function and homology information
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å
AuthorsSchumacher, M.A.
CitationJournal: Rna / Year: 2020
Title: Structures of MERS1, the 5' processing enzyme of mitochondrial mRNAs inTrypanosoma brucei.
Authors: Schumacher, M.A. / Henderson, M. / Zeng, W.
History
DepositionMay 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Mitochondrial edited mRNA stability factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4002
Polymers45,9561
Non-polymers4431
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Mitochondrial edited mRNA stability factor 1
hetero molecules

A: Mitochondrial edited mRNA stability factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7994
Polymers91,9132
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5120 Å2
ΔGint-22 kcal/mol
Surface area26350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.815, 114.453, 77.964
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Mitochondrial edited mRNA stability factor 1


Mass: 45956.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: MERS1 / Production host: Escherichia coli (E. coli) / References: UniProt: B6SBM0
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Peg 3350, Magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→77.9 Å / Num. obs: 14927 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.031 / Net I/σ(I): 12
Reflection shellResolution: 2.45→2.529 Å / Redundancy: 4 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1199 / CC1/2: 0.965 / Rpim(I) all: 0.217 / % possible all: 94

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.45→35.173 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.97
RfactorNum. reflection% reflection
Rfree0.2562 1494 10.01 %
Rwork0.2268 --
obs0.2298 14927 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.22 Å2 / Biso mean: 78.7047 Å2 / Biso min: 42.68 Å2
Refinement stepCycle: final / Resolution: 2.45→35.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 28 10 2508
Biso mean--116.6 61 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032570
X-RAY DIFFRACTIONf_angle_d0.6663509
X-RAY DIFFRACTIONf_chiral_restr0.044375
X-RAY DIFFRACTIONf_plane_restr0.003448
X-RAY DIFFRACTIONf_dihedral_angle_d5.1811535
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.52910.36691210.36381089121088
2.5291-2.61940.34321320.32051184131696
2.6194-2.72430.38011350.31531218135399
2.7243-2.84820.31261360.29111215135199
2.8482-2.99830.31821360.27512351371100
2.9983-3.1860.31931380.2751233137199
3.186-3.43190.28191370.26231238137599
3.4319-3.77690.29351390.236812521391100
3.7769-4.32250.25161400.197412591399100
4.3225-5.44270.18471400.17331252139299
5.4427-35.17690.21181400.20091258139894
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8262-4.4269-1.79627.94161.08884.26110.3193-1.02920.5769-0.25390.6614-0.49560.06951.1218-0.30120.6438-0.09980.02841.25570.04470.87-6.181-1.074-8.826
23.7631-0.0274.31356.7448-3.01126.3723-0.295-0.2017-0.83860.36650.3071-2.4104-0.26741.10970.14770.64030.21350.14371.26360.03570.9166-3.525-10.734-13.348
30.225-0.143-0.27470.33260.03860.898-0.11340.30710.6463-0.6645-0.5173-0.0921-0.1787-0.2505-0.02331.30110.1120.12950.87340.12020.7861-12.09111.678-19.262
42.1604-0.3061.52965.51560.31053.6390.02070.3430.3075-0.9121-0.1972-0.2594-0.31370.0520.21970.59660.02390.02050.44780.03940.39-18.0942.56-16.679
52.4487-0.15210.71873.9382-0.08864.4794-0.11630.105-0.2726-0.5973-0.073-0.39830.62030.16910.17480.69030.01030.13610.4807-0.01290.4701-18.075-20.333-9.323
63.468-0.12422.00953.07241.67394.08540.1939-0.1292-0.53270.1483-0.1862-0.43420.89850.13910.04210.9533-0.00710.02710.60440.11510.7157-16.285-27.3960.823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 331:337 )A331 - 337
2X-RAY DIFFRACTION2( CHAIN A AND RESID 338:345 )A338 - 345
3X-RAY DIFFRACTION3( CHAIN A AND RESID 406:424 )A406 - 424
4X-RAY DIFFRACTION4( CHAIN A AND RESID 426:522 )A426 - 522
5X-RAY DIFFRACTION5( CHAIN A AND RESID 523:623 )A523 - 623
6X-RAY DIFFRACTION6( CHAIN A AND RESID 624:710 )A624 - 710

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