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- PDB-5bjr: Crystal structure of the N-terminal RRM domain from MEC-8 -

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Basic information

Entry
Database: PDB / ID: 5bjr
TitleCrystal structure of the N-terminal RRM domain from MEC-8
ComponentsMec-8 protein
KeywordsSPLICING / alternative splicing / mRNA / RNA-binding protein
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 / 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
AMMONIUM ION / Mec-8 protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Jan 10, 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

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Assembly

Deposited unit
A: Mec-8 protein
B: Mec-8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6865
Polymers20,6322
Non-polymers543
Water66737
1
A: Mec-8 protein
hetero molecules

A: Mec-8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7046
Polymers20,6322
Non-polymers724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area1000 Å2
ΔGint-5 kcal/mol
Surface area10660 Å2
MethodPISA
2
B: Mec-8 protein
hetero molecules

B: Mec-8 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6684
Polymers20,6322
Non-polymers362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area1160 Å2
ΔGint-2 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.590, 96.420, 109.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Mec-8 protein


Mass: 10315.975 Da / Num. of mol.: 2 / Fragment: N-terminal RRM residues 28-117 / Mutation: C54A,C102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mec-8, CELE_F46A9.6, F46A9.6 / Plasmid: pET-His1a / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): LysY / References: UniProt: G5ECJ4
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.38 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M sodium acetate pH 6.5, 0.2 M ammonium sulfate, PEG 4000 30% w/v

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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: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.6→35.36 Å / Num. obs: 8842 / % possible obs: 98.93 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.08528 / Net I/σ(I): 6
Reflection shellResolution: 2.6→2.76 Å / Rmerge(I) obs: 0.3439

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Processing

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

3md1


Resolution: 2.6→35.36 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.68
RfactorNum. reflection% reflection
Rfree0.2853 886 10.02 %
Rwork0.2372 --
obs0.2421 8842 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 3 37 1368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021350
X-RAY DIFFRACTIONf_angle_d0.5711813
X-RAY DIFFRACTIONf_dihedral_angle_d8.917525
X-RAY DIFFRACTIONf_chiral_restr0.022200
X-RAY DIFFRACTIONf_plane_restr0.002237
LS refinement shellResolution: 2.6002→2.763 Å /
Num. reflection% reflection
Rfree146 -
Rwork1316 -
obs-99 %

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