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- PDB-1oxj: Crystal structure of the Smaug RNA binding domain -

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Basic information

Entry
Database: PDB / ID: 1oxj
TitleCrystal structure of the Smaug RNA binding domain
ComponentsRNA-binding protein Smaug
KeywordsRNA BINDING PROTEIN / SAM domain / PHAT domain / RNA-binding protein
Function / homology
Function and homology information


establishment of RNA localization / nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / myosin binding / translation repressor activity / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / P-body / negative regulation of translation ...establishment of RNA localization / nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / myosin binding / translation repressor activity / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / P-body / negative regulation of translation / mRNA binding / regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Smaug, PHAT domain / Smaug, PHAT analogous topology / PHAT / Smaug, PHAT domain superfamily / Protein Smaug, SAM domain / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily ...Smaug, PHAT domain / Smaug, PHAT analogous topology / PHAT / Smaug, PHAT domain superfamily / Protein Smaug, SAM domain / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / DNA polymerase; domain 1 / Alpha Horseshoe / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsGreen, J.B. / Gardner, C.D. / Wharton, R.P. / Aggarwal, A.K.
CitationJournal: Mol.Cell / Year: 2003
Title: RNA recognition via the SAM domain of Smaug.
Authors: Green, J.B. / Gardner, C.D. / Wharton, R.P. / Aggarwal, A.K.
History
DepositionApr 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE His tag is removed leaving the non-smg sequence GTHM on the N-terminal end.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein Smaug


Theoretical massNumber of molelcules
Total (without water)19,6761
Polymers19,6761
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.320, 129.320, 33.125
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein RNA-binding protein Smaug


Mass: 19675.971 Da / Num. of mol.: 1 / Fragment: RNA binding domain, SAM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: SMG / Plasmid: pET 15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q23972
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, Sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117 %PEG40001reservoir
2220 mMsodium acetate1reservoir
3100 mMTris-Cl1reservoirpH8.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11701
21701
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.94207, 0.97941, 0.97927
SYNCHROTRONNSLS X2520.9188
Detector
TypeIDDetectorDate
SBC-21CCDMar 1, 2001
BRANDEIS - B42CCDApr 13, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)MADMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.942071
20.979411
30.979271
40.91881
ReflectionResolution: 1.8→50 Å / Num. obs: 19192 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.036 / Net I/σ(I): 34.9
Reflection shellResolution: 1.8→50 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.2 / % possible all: 74.6
Reflection
*PLUS
Num. measured all: 151643
Reflection shell
*PLUS
% possible obs: 74.6 % / Rmerge(I) obs: 0.33

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1257 -random
Rwork0.229 ---
all0.231 19192 --
obs0.231 18277 88.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1355 0 0 163 1518
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00766
X-RAY DIFFRACTIONc_angle_deg1.01337
X-RAY DIFFRACTIONc_dihedral_angle_d18.5541
X-RAY DIFFRACTIONc_improper_angle_d0.6956
X-RAY DIFFRACTIONc_mcbond_it1.407
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.8-1.860.37611070.36130.77135270.27
1.86-1.940.37871210.31770.79157381.17
1.94-2.030.29111050.29090.85173791.66
2.03-2.130.26551310.27080.89174691.7
2.13-2.270.29811280.25990.86180793.24
2.27-2.440.2931300.24360.88177393.02
Refinement
*PLUS
% reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.5541
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.6956

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