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- PDB-5tkz: MEC-8 N-terminal RRM bound to tandem GCAC ligand -

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Basic information

Entry
Database: PDB / ID: 5tkz
TitleMEC-8 N-terminal RRM bound to tandem GCAC ligand
Components
  • DNA (5'-D(*AP*GP*CP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*TP*AP*GP*CP*AP*CP*A)-3')
  • Mec-8 protein
KeywordsSPLICING / Alternative splicing / RRM / DNA / elegans
Function / homology
Function and homology information


nematode larval development / muscle organ morphogenesis / hemidesmosome assembly / mechanosensory behavior / embryo development ending in birth or egg hatching / neuron development / mRNA binding / RNA binding / nucleus
Similarity search - Function
Protein couch potato, RNA recognition motif / 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
DNA / DNA (> 10) / Mec-8 protein / Mec-8 protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.529 Å
AuthorsSoufari, H. / Mackereth, C.D.
CitationJournal: RNA / Year: 2017
Title: Conserved binding of GCAC motifs by MEC-8, couch potato, and the RBPMS protein family.
Authors: Soufari, H. / Mackereth, C.D.
History
DepositionOct 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Source and taxonomy / Structure summary
Revision 1.2Mar 1, 2017Group: Database references
Revision 1.3Feb 20, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn / pdbx_seq_map_depositor_info
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Jan 17, 2024Group: 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: Mec-8 protein
B: Mec-8 protein
C: DNA (5'-D(*AP*GP*CP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*TP*AP*GP*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)26,7153
Polymers26,7153
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint4 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.188, 52.188, 156.534
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-234-

HOH

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Components

#1: Protein Mec-8 protein


Mass: 10315.975 Da / Num. of mol.: 2 / Mutation: C54A, C102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mec-8 / Plasmid: pET His 1a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Lys Y / References: UniProt: Q22039, UniProt: G5ECJ4*PLUS
#2: DNA chain DNA (5'-D(*AP*GP*CP*AP*CP*AP*TP*TP*TP*TP*TP*TP*TP*TP*AP*GP*CP*AP*CP*A)-3')


Mass: 6082.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.89 Å3/Da / Density % sol: 35.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000 10% (v/v), isopropanol 10%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.529→25.74 Å / Num. obs: 38386 / % possible obs: 99.99 % / Redundancy: 2 % / Rmerge(I) obs: 0.03396 / Net I/σ(I): 8.03
Reflection shellResolution: 1.529→1.584 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3595 / Mean I/σ(I) obs: 2.26 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MD1

3md1


Resolution: 1.529→25.736 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.66
RfactorNum. reflection% reflection
Rfree0.2711 2009 5.23 %
Rwork0.2327 --
obs0.2347 38385 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.529→25.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1382 206 0 134 1722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091654
X-RAY DIFFRACTIONf_angle_d1.1772270
X-RAY DIFFRACTIONf_dihedral_angle_d19.504648
X-RAY DIFFRACTIONf_chiral_restr0.048254
X-RAY DIFFRACTIONf_plane_restr0.006262
LS refinement shellResolution: 1.529→1.58 Å
Refinement TLS params.Method: refined / Origin x: -10.5793 Å / Origin y: 36.8055 Å / Origin z: 77.841 Å
111213212223313233
T0.4019 Å2-0.1865 Å20.0289 Å2-0.258 Å2-0.0209 Å2--0.1442 Å2
L0.1851 °20.1576 °20.0088 °2-0.3432 °20.0018 °2--0.0588 °2
S-0.0266 Å °0.0382 Å °0.0052 Å °-0.0217 Å °0.0241 Å °0.0063 Å °-0.005 Å °-0.0093 Å °0.0495 Å °
Refinement TLS groupSelection details: all

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