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- PDB-3n8b: Crystal Structure of Borrelia burgdorferi Pur-alpha -

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Basic information

Entry
Database: PDB / ID: 3n8b
TitleCrystal Structure of Borrelia burgdorferi Pur-alpha
ComponentsUncharacterized protein
KeywordsNUCLEIC ACID BINDING PROTEIN / Pur-alpha / Pur repeat / Pur domain / Whirly fold / RNA binding / DNA binding
Function / homology
Function and homology information


purine-rich negative regulatory element binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / metal ion binding
Similarity search - Function
Protein of unknown function DUF3276 / Protein of unknown function (DUF3276) / Nuclear Transport Factor 2; Chain: A, - #700 / 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
DUF3276 family protein
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsGraebsch, A. / Roche, S. / Kostrewa, D. / Niessing, D.
Citation
Journal: Plos One / Year: 2010
Title: Of bits and bugs--on the use of bioinformatics and a bacterial crystal structure to solve a eukaryotic repeat-protein structure.
Authors: Graebsch, A. / Roche, S. / Kostrewa, D. / Soding, J. / Niessing, D.
#1: Journal: 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
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Feb 28, 2018Group: Advisory / Category: pdbx_unobs_or_zero_occ_atoms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3358
Polymers23,0392
Non-polymers2976
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-27 kcal/mol
Surface area9080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.710, 58.330, 141.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-108-

MG

21B-106-

MG

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Components

#1: Protein Uncharacterized protein


Mass: 11519.287 Da / Num. of mol.: 2 / Fragment: Pur-alpha residues 8-105 / Mutation: L17M, F27M, I64M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: BB_0047 / Plasmid: pGEX6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O51076
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 277 K / pH: 8
Details: 125 mM NaCl, 10 mM Hepes pH 8.0, 2.8 M sodium formate, equimolar addition of DNA oligonucleotide 5'AGG GTT AGG GTT-3' (not visible in structure), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9792
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 20, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→70.946 Å / Num. obs: 30605 / % possible obs: 98.7 % / Observed criterion σ(I): 5 / Redundancy: 3.5 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.082 / Net I/σ(I): 12.9
Reflection scaleGroup code: 1
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.35 / % possible all: 95.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SHELXphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→37.39 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.187 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.232 816 5 %RANDOM
Rwork0.185 ---
obs0.187 30605 99.3 %-
all-31023 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å20 Å2
2---0.75 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 18 149 1416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221335
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.9541790
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9845166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37924.73776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89615264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.877159
X-RAY DIFFRACTIONr_chiral_restr0.0880.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021021
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0572769
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.01731254
X-RAY DIFFRACTIONr_scbond_it2.9694.5566
X-RAY DIFFRACTIONr_scangle_it4.9016526
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 50 -
Rwork0.226 1145 -
obs--98.11 %

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