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- PDB-3bwt: Crystal structure of the RNA binding domain of Puf4 from Saccharo... -

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Basic information

Entry
Database: PDB / ID: 3bwt
TitleCrystal structure of the RNA binding domain of Puf4 from Saccharomyces cerevisiae
ComponentsProtein PUF4
KeywordsTRANSCRIPTION / RNA BINDING PROTEIN / Puf4 / Pumilio / RNA Binding / HO endonuclease
Function / homology
Function and homology information


nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / post-transcriptional regulation of gene expression / protein localization / negative regulation of translation / mRNA binding / 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
Pumilio homology domain family member 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsMiller, M.T. / Higgin, J.J. / Hall, T.M.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p
Authors: Miller, M.T. / Higgin, J.J. / Hall, T.M.T.
History
DepositionJan 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Protein PUF4


Theoretical massNumber of molelcules
Total (without water)37,7651
Polymers37,7651
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.188, 137.657, 137.542
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein PUF4


Mass: 37765.414 Da / Num. of mol.: 1 / Fragment: Single Stranded RNA Binding Domin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PUF4 / Production host: Escherichia coli (E. coli) / References: UniProt: P25339
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.4 Å3/Da / Density % sol: 63.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1.2 M ammonium sulfate, 100 mM Na cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Aug 31, 2006
RadiationMonochromator: varimax hf / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.69→31.2 Å / Num. all: 15038 / Num. obs: 14317 / % possible obs: 97 % / Observed criterion σ(I): 1
Reflection shellResolution: 2.69→2.8 Å / % possible all: 95.2

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Processing

Software
NameClassification
CrystalCleardata collection
SOLVEphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→31.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 721 5 %Random
Rwork0.2 ---
all0.201 14317 --
obs0.201 14317 --
Refinement stepCycle: LAST / Resolution: 2.69→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 0 55 2704
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONf_bond_d0.008273.555
X-RAY DIFFRACTIONf_angle_d1.062866.476
X-RAY DIFFRACTIONf_chiral_restr0.222527.156
X-RAY DIFFRACTIONf_planar_d0.00459.397
X-RAY DIFFRACTIONf_planar_tor18.771542.074
X-RAY DIFFRACTIONf_hb_or_metal_coord4.108414.307
LS refinement shellResolution: 2.69→2.72 Å
RfactorNum. reflection% reflection
Rfree0.39 20 -
Rwork0.24 --
obs-402 76 %

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