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- PDB-5d77: Structure of Mip6 RRM3 Domain -

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Basic information

Entry
Database: PDB / ID: 5d77
TitleStructure of Mip6 RRM3 Domain
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
CITRIC ACID / NITRATE ION / RNA-binding protein MIP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMohamad, N. / Bravo, J.
CitationJournal: To Be Published
Title: Structure of Mip6 RRM3 domain at 1.3
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)9,5515
Polymers9,2121
Non-polymers3394
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint1 kcal/mol
Surface area5210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.310, 36.310, 91.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 9211.569 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.64 Å3/Da / Density % sol: 25.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 1.6M Sodium Citrate Tribasic dihydrate pH 6.5; Ammonium Nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.3→45.91 Å / Num. obs: 15814 / % possible obs: 99.4 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.45 / Net I/σ(I): 25.1
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.5 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FEY

3fey


Resolution: 1.3→33.766 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1818 782 4.97 %
Rwork0.1514 --
obs0.1529 15738 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→33.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms647 0 22 51 720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009699
X-RAY DIFFRACTIONf_angle_d1.278944
X-RAY DIFFRACTIONf_dihedral_angle_d19.177276
X-RAY DIFFRACTIONf_chiral_restr0.077103
X-RAY DIFFRACTIONf_plane_restr0.006121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.38150.26031160.17412324X-RAY DIFFRACTION95
1.3815-1.48810.20861240.1592450X-RAY DIFFRACTION100
1.4881-1.63790.23451310.14872475X-RAY DIFFRACTION100
1.6379-1.87490.19111390.14462476X-RAY DIFFRACTION100
1.8749-2.3620.18671320.14722529X-RAY DIFFRACTION100
2.362-33.77690.16511400.15272702X-RAY DIFFRACTION100

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