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- PDB-6y6e: drosophila Unr CSD456 -

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Basic information

Entry
Database: PDB / ID: 6y6e
Titledrosophila Unr CSD456
ComponentsUpstream of N-ras, isoform A
KeywordsRNA BINDING PROTEIN / CSD / ncCSD
Function / homology
Function and homology information


nucleic acid binding
Similarity search - Function
Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
ETHYL MERCURY ION / Upstream of N-ras, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.02 Å
AuthorsHollmann, N.M. / Jagtap, P.K.A. / Hennig, J.
CitationJournal: Cell Rep / Year: 2020
Title: Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras.
Authors: Hollmann, N.M. / Jagtap, P.K.A. / Masiewicz, P. / Guitart, T. / Simon, B. / Provaznik, J. / Stein, F. / Haberkant, P. / Sweetapple, L.J. / Villacorta, L. / Mooijman, D. / Benes, V. / ...Authors: Hollmann, N.M. / Jagtap, P.K.A. / Masiewicz, P. / Guitart, T. / Simon, B. / Provaznik, J. / Stein, F. / Haberkant, P. / Sweetapple, L.J. / Villacorta, L. / Mooijman, D. / Benes, V. / Savitski, M.M. / Gebauer, F. / Hennig, J.
History
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Upstream of N-ras, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3645
Polymers29,4451
Non-polymers9194
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-13 kcal/mol
Surface area14070 Å2
Unit cell
Length a, b, c (Å)89.880, 89.880, 58.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-581-

HOH

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Components

#1: Protein Upstream of N-ras, isoform A


Mass: 29445.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Unr, BcDNA:LD13080, CR32028, Dmel\CG7015, dUNR, MRE30, UNR, unr, CG7015, Dmel_CG7015
Variant: isoform A / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9VSK3
#2: Chemical
ChemComp-EMC / ETHYL MERCURY ION / Ethylmercury


Mass: 229.651 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M tri-sodium citrate (pH 5.5), 20% PEG2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.005 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 29, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.02→77.84 Å / Num. obs: 17627 / % possible obs: 98.71 % / Redundancy: 6.5 % / Biso Wilson estimate: 39.76 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.037 / Rrim(I) all: 0.095 / Net I/σ(I): 11.06
Reflection shellResolution: 2.02→2.092 Å / Redundancy: 5 % / Rmerge(I) obs: 0.86 / Num. unique obs: 1595 / CC1/2: 0.65 / Rpim(I) all: 0.41 / Rrim(I) all: 0.96 / % possible all: 90.07

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.02→77.84 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2513 1698 -
Rwork0.2153 --
obs-34126 98.7 %
Displacement parametersBiso mean: 47.73 Å2
Refinement stepCycle: LAST / Resolution: 2.02→77.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 7 213 2062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00151873
X-RAY DIFFRACTIONf_angle_d0.38192524
X-RAY DIFFRACTIONf_chiral_restr0.0414290
X-RAY DIFFRACTIONf_plane_restr0.0023327
X-RAY DIFFRACTIONf_dihedral_angle_d16.6664684

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