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- PDB-3k44: Crystal Structure of Drosophila melanogaster Pur-alpha -

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Basic information

Entry
Database: PDB / ID: 3k44
TitleCrystal Structure of Drosophila melanogaster Pur-alpha
ComponentsPurine-rich binding protein-alpha, isoform B
KeywordsNUCLEIC ACID BINDING PROTEIN / Pur-alpha / Pur repeat / Pur domain / Whirly fold / DNA BINDING PROTEIN / RNA BINDING PROTEIN
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
Secreted effector protein pipB2 fold - #30 / Secreted effector protein pipB2 fold / 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. / 2-Layer Sandwich / 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 / MAD / Resolution: 2.1 Å
AuthorsGraebsch, A. / Roche, S. / Niessing, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: X-ray structure of Pur-alpha reveals a Whirly-like fold and an unusual nucleic-acid binding surface
Authors: Graebsch, A. / Roche, S. / Niessing, D.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine-rich binding protein-alpha, isoform B
B: Purine-rich binding protein-alpha, isoform B
C: Purine-rich binding protein-alpha, isoform B
D: Purine-rich binding protein-alpha, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,65616
Polymers67,1244
Non-polymers53212
Water2,810156
1
A: Purine-rich binding protein-alpha, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0126
Polymers16,7811
Non-polymers2305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Purine-rich binding protein-alpha, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8162
Polymers16,7811
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Purine-rich binding protein-alpha, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0126
Polymers16,7811
Non-polymers2305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Purine-rich binding protein-alpha, isoform B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8162
Polymers16,7811
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.168, 62.544, 64.479
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11B-196-

HOH

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Components

#1: Protein
Purine-rich binding protein-alpha, isoform B


Mass: 16781.027 Da / Num. of mol.: 4 / Fragment: sequence database residues 40-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG1507, Dmel_CG1507, Pur-alpha / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9V4D9, UniProt: Q95RR6*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.935.17
2
Crystal grow
Temperature (K)Crystal-IDMethodDetailsPH range
2981vapor diffusion, hanging drop50 mM Mes, 200 mM MgCl2, 25% PEG 3350, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K5.9; 7.8
2982vapor diffusion, hanging drop100 mM HEPES, 200 mM MgCl2, 22% PEG 3350, 1 mM DTT, 1 mM TCEP, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONESRF ID14-420.979, 0.979, 0.957
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDDec 4, 2008
ADSC QUANTUM 315r2CCDMay 1, 2009
Radiation
IDProtocolScattering typeWavelength-IDMonochromatic (M) / Laue (L)
1SINGLE WAVELENGTHx-ray1
2MADx-ray2M
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
20.9791
30.9571
ReflectionResolution: 2.1→64.479 Å / Num. obs: 28601 / % possible obs: 98.9 % / Observed criterion σ(I): 4.35
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 5.65 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 4.35 / Rsym value: 0.403 / % possible all: 94.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
CRUNCH2model building
REFMAC5refinement
XDSdata reduction
XSCALEdata scaling
CRUNCH2phasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→44.46 Å / σ(F): 4.35 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1500 -RANDOM
Rwork0.222 ---
obs0.223 28601 98.9 %-
all-28910 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å2-0.03 Å2
2---2.38 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4654 0 24 156 4834

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