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- PDB-7e4v: Crystal structure of mosquito Staufen dsRNA binding domain 4 -

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Basic information

Entry
Database: PDB / ID: 7e4v
TitleCrystal structure of mosquito Staufen dsRNA binding domain 4
ComponentsStaufen
KeywordsRNA BINDING PROTEIN / Staufen / RNA-binding
Function / homologyStaufen, C-terminal / Staufen C-terminal domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / RNA binding / AAEL007470-PA
Function and homology information
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsGayathiri, S.K. / Jobichen, C. / Mok, Y.K.
CitationJournal: To Be Published
Title: Crystal structure of mosquito Staufen dsRNA binding domain 4
Authors: Gayathiri, S.K. / Jobichen, C. / Mok, Y.K.
History
DepositionFeb 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Staufen
B: Staufen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7323
Polymers16,6392
Non-polymers921
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint0 kcal/mol
Surface area8910 Å2
Unit cell
Length a, b, c (Å)42.528, 42.528, 155.611
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 18 and (name N or name...
21(chain B and (resid 18 through 46 or resid 48...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMET(chain A and ((resid 18 and (name N or name...AA182
12METMETSERSER(chain A and ((resid 18 and (name N or name...AA18 - 912 - 75
13METMETSERSER(chain A and ((resid 18 and (name N or name...AA18 - 912 - 75
14METMETSERSER(chain A and ((resid 18 and (name N or name...AA18 - 912 - 75
15METMETSERSER(chain A and ((resid 18 and (name N or name...AA18 - 912 - 75
21METMETGLYGLY(chain B and (resid 18 through 46 or resid 48...BB18 - 462 - 30
22ALAALAALAALA(chain B and (resid 18 through 46 or resid 48...BB4832
23ARGARGARGARG(chain B and (resid 18 through 46 or resid 48...BB5135
24GLYGLYSERSER(chain B and (resid 18 through 46 or resid 48...BB17 - 911 - 75
25GLYGLYSERSER(chain B and (resid 18 through 46 or resid 48...BB17 - 911 - 75
26GLYGLYSERSER(chain B and (resid 18 through 46 or resid 48...BB17 - 911 - 75
27GLYGLYSERSER(chain B and (resid 18 through 46 or resid 48...BB17 - 911 - 75

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Components

#1: Protein Staufen / AAEL007470-PA


Mass: 8319.749 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: AAEL007470
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q172A2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / Details: PEG3350 25%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 34672 / % possible obs: 97.9 % / Redundancy: 10.6 % / Rpim(I) all: 0.033 / Net I/σ(I): 37.3
Reflection shellResolution: 1.37→1.39 Å / Num. unique obs: 1364 / Rpim(I) all: 0.398

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CFF

5cff


Resolution: 1.37→36.83 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 1988 5.74 %
Rwork0.1921 32622 -
obs0.1932 34610 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.03 Å2 / Biso mean: 21.2013 Å2 / Biso min: 10.96 Å2
Refinement stepCycle: final / Resolution: 1.37→36.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 6 230 1345
Biso mean--26.02 32.11 -
Num. residues----149
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A390X-RAY DIFFRACTION6.387TORSIONAL
12B390X-RAY DIFFRACTION6.387TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.37-1.410.29461160.31411887200382
1.41-1.440.30881310.26882186231794
1.44-1.490.24281470.214423312478100
1.49-1.530.21641430.197623362479100
1.53-1.590.21971340.1812339247399
1.59-1.650.20091460.190623332479100
1.65-1.730.19811360.18272319245599
1.73-1.820.21921430.204123672510100
1.82-1.930.23151440.178923902534100
1.93-2.080.1651470.173523552502100
2.08-2.290.18811460.17082362250899
2.29-2.620.1921500.197424222572100
2.62-3.30.2151500.200224382588100
3.3-36.830.231550.18922557271299
Refinement TLS params.Method: refined / Origin x: 17.9335 Å / Origin y: -13.3847 Å / Origin z: -12.0655 Å
111213212223313233
T0.1291 Å20.0165 Å2-0.0034 Å2-0.1321 Å20.0089 Å2--0.1371 Å2
L0.068 °20.0466 °2-0.1164 °2-0.167 °20.0014 °2--0.4754 °2
S-0.0017 Å °0.0092 Å °0.0145 Å °-0.0232 Å °-0.023 Å °0.0046 Å °-0.0105 Å °-0.0278 Å °0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA18 - 91
2X-RAY DIFFRACTION1allB17 - 91
3X-RAY DIFFRACTION1allS225 - 241

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