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- PDB-5fgo: Crystal structure of D. melanogaster Pur-alpha repeat III. -

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Basic information

Entry
Database: PDB / ID: 5fgo
TitleCrystal structure of D. melanogaster Pur-alpha repeat III.
ComponentsCG1507-PB, isoform B
KeywordsDNA BINDING PROTEIN / DNA-protein interaction / RNA-protein interaction / DNA unwinding / FXTAS / ALS / FTLD / 5q31.3 microdeletion syndrome / neurodegeneration
Function / homology
Function and homology information


purine-rich negative regulatory element binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / mRNA binding / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Nuclear Transport Factor 2; Chain: A, - #700 / PurA ssDNA and RNA-binding protein / Purine-rich element binding protein family / DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria. / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
LD15002p / Purine-rich binding protein-alpha, isoform B
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWindhager, A. / Janowski, R. / Niessing, D.
CitationJournal: Elife / Year: 2016
Title: Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alpha.
Authors: Weber, J. / Bao, H. / Hartlmuller, C. / Wang, Z. / Windhager, A. / Janowski, R. / Madl, T. / Jin, P. / Niessing, D.
History
DepositionDec 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CG1507-PB, isoform B
B: CG1507-PB, isoform B
C: CG1507-PB, isoform B
D: CG1507-PB, isoform B
E: CG1507-PB, isoform B
F: CG1507-PB, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2628
Polymers58,1916
Non-polymers712
Water3,063170
1
A: CG1507-PB, isoform B
B: CG1507-PB, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4323
Polymers19,3972
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-43 kcal/mol
Surface area8140 Å2
MethodPISA
2
C: CG1507-PB, isoform B
D: CG1507-PB, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4323
Polymers19,3972
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-40 kcal/mol
Surface area8410 Å2
MethodPISA
3
E: CG1507-PB, isoform B
F: CG1507-PB, isoform B


Theoretical massNumber of molelcules
Total (without water)19,3972
Polymers19,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-38 kcal/mol
Surface area8250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.460, 55.530, 67.840
Angle α, β, γ (deg.)90.00, 95.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CG1507-PB, isoform B / Purine-rich binding protein-alpha / isoform F / Pur-alpha repeat III


Mass: 9698.516 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Pur-alpha, CG1507, Dmel_CG1507 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V4D9, UniProt: Q95RR6*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 50 mM MES pH 6.5, 200 mM NaCl, 16% PEG 3350 and 6 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 9, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 13999 / % possible obs: 96.5 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.4
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.97 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N8B

3n8b


Resolution: 2.6→47.725 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2885 1319 4.98 %
Rwork0.2019 --
obs0.206 13999 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→47.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 2 170 3471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113417
X-RAY DIFFRACTIONf_angle_d1.3574560
X-RAY DIFFRACTIONf_dihedral_angle_d14.0041353
X-RAY DIFFRACTIONf_chiral_restr0.061443
X-RAY DIFFRACTIONf_plane_restr0.007595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70410.32661450.27982770X-RAY DIFFRACTION95
2.7041-2.82720.34171550.2512874X-RAY DIFFRACTION99
2.8272-2.97620.27571630.23332805X-RAY DIFFRACTION99
2.9762-3.16270.37561410.22552885X-RAY DIFFRACTION99
3.1627-3.40680.27761410.22862X-RAY DIFFRACTION98
3.4068-3.74950.28871330.19722584X-RAY DIFFRACTION89
3.7495-4.29180.26321390.18052666X-RAY DIFFRACTION92
4.2918-5.4060.24241610.15082840X-RAY DIFFRACTION99
5.406-100.30251410.21242866X-RAY DIFFRACTION98

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