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- PDB-5d78: Structure of RRM3 Domain of Mip6 at 1.25 A Resolution -

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Basic information

Entry
Database: PDB / ID: 5d78
TitleStructure of RRM3 Domain of Mip6 at 1.25 A Resolution
ComponentsRNA-binding protein MIP6
KeywordsRNA BINDING PROTEIN / RNA Binding Domain
Function / homology
Function and homology information


mRNA localization resulting in post-transcriptional regulation of gene expression / mRNA metabolic process / sporulation / prospore membrane / poly(A) binding / poly(U) RNA binding / mRNA 3'-UTR binding / cytoplasmic stress granule / regulation of translation / ribonucleoprotein complex ...mRNA localization resulting in post-transcriptional regulation of gene expression / mRNA metabolic process / sporulation / prospore membrane / poly(A) binding / poly(U) RNA binding / mRNA 3'-UTR binding / cytoplasmic stress granule / regulation of translation / ribonucleoprotein complex / RNA binding / nucleus / cytosol
Similarity search - Function
: / 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
BETA-MERCAPTOETHANOL / RNA-binding protein MIP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.251 Å
AuthorsMohamad, N. / Bravo, J.
CitationJournal: To Be Published
Title: Structure of RRM3 Domain of Mip6 at 1.25 A Resolution
Authors: Mohamad, N. / Bravo, J.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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: RNA-binding protein MIP6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3634
Polymers9,1101
Non-polymers2523
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-7 kcal/mol
Surface area5150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.842, 47.023, 30.563
Angle α, β, γ (deg.)90.00, 109.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA-binding protein MIP6 / MEX67-interacting protein 6


Mass: 9110.442 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: MIP6, YHR015W / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon plus / References: UniProt: P38760
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M Lithium Sulfate; 0.1 M tris pH 8.5; 40% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97947 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.25→47.02 Å / Num. obs: 14132 / % possible obs: 74.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.31 / Net I/σ(I): 24.6
Reflection shellResolution: 1.25→1.27 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5d77

5d77


Resolution: 1.251→28.758 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 23.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1771 716 5.07 %
Rwork0.1371 --
obs0.1391 14114 73.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.251→28.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms640 0 13 99 752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009664
X-RAY DIFFRACTIONf_angle_d1.254892
X-RAY DIFFRACTIONf_dihedral_angle_d12.621248
X-RAY DIFFRACTIONf_chiral_restr0.079100
X-RAY DIFFRACTIONf_plane_restr0.006110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2508-1.34740.3372390.2039662X-RAY DIFFRACTION19
1.3474-1.48290.195980.15422056X-RAY DIFFRACTION57
1.4829-1.69750.18791870.14143451X-RAY DIFFRACTION96
1.6975-2.13860.18211910.13553590X-RAY DIFFRACTION99
2.1386-28.76570.1662010.1333639X-RAY DIFFRACTION99

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