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- PDB-3qgb: Crystal structure of FBF-2 R288Y mutant in complex with gld-1 FBEa -

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Basic information

Entry
Database: PDB / ID: 3qgb
TitleCrystal structure of FBF-2 R288Y mutant in complex with gld-1 FBEa
Components
  • 5'-R(*UP*GP*UP*GP*CP*CP*AP*UP*A)-3'
  • Fem-3 mRNA-binding factor 2
KeywordsRNA BINDING PROTEIN/RNA / FBF / FEM-3 BINDING FACTOR / PUF / RNA-BINDING SPECIFICITY / BASE STACKING / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


sex differentiation / P granule / post-transcriptional regulation of gene expression / mRNA 3'-UTR binding / cell differentiation / negative regulation of translation / RNA binding / nucleus / cytoplasm
Similarity search - Function
Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical ...Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
RNA / Fem-3 mRNA-binding factor 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, Y. / Qiu, C. / Koh, Y.Y. / Opperman, L. / Gross, L. / Hall, T.M.T. / Wickens, M.
CitationJournal: Rna / Year: 2011
Title: Stacking interactions in PUF-RNA complexes.
Authors: Koh, Y.Y. / Wang, Y. / Qiu, C. / Opperman, L. / Gross, L. / Tanaka Hall, T.M. / Wickens, M.
History
DepositionJan 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fem-3 mRNA-binding factor 2
B: 5'-R(*UP*GP*UP*GP*CP*CP*AP*UP*A)-3'


Theoretical massNumber of molelcules
Total (without water)49,8582
Polymers49,8582
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-6 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.809, 96.809, 100.895
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Fem-3 mRNA-binding factor 2


Mass: 47025.035 Da / Num. of mol.: 1 / Fragment: PUM-HD domain, rsidues 164-575 / Mutation: R288Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: fbf-2, F21H12.5 / Plasmid: pGex6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q09312
#2: RNA chain 5'-R(*UP*GP*UP*GP*CP*CP*AP*UP*A)-3'


Mass: 2832.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic RNA
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.74 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 MM TRIS PH 7.5, 10% POLYETHYLENE GLYCOL 8000, AND 8% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→43.64 Å / Num. all: 21359 / Num. obs: 21358 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.2 % / Biso Wilson estimate: 28.462 Å2 / Rsym value: 0.174 / Net I/σ(I): 18.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1069 / Rsym value: 0.903 / % possible all: 100

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Processing

Software
NameClassification
SERGUIdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K5Y

3k5y


Resolution: 2.4→43.64 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1089 -based on the mtz file of PDB ENTRY 3K5Y
Rwork0.168 ---
all0.186 21359 --
obs-21358 100 %-
Displacement parametersBiso mean: 34.7345 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-1.03 Å22.059 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 187 0 298 3668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_deg0.607
X-RAY DIFFRACTIONf_dihedral_angle_d10.653

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