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- PDB-3ra0: Crystal Structure of a StWhy2 K67A-dT32 complex -

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Basic information

Entry
Database: PDB / ID: 3ra0
TitleCrystal Structure of a StWhy2 K67A-dT32 complex
Components
  • DNA 32-mer dT32
  • Why2 protein
KeywordsDNA BINDING PROTEIN/DNA / StWhy2 / single-stranded DNA binding protein / Plant / Potato / Whirly / protein-DNA complex / Mitochondria / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


defense response / single-stranded DNA binding / DNA repair / regulation of DNA-templated transcription / mitochondrion / DNA binding
Similarity search - Function
Whirly transcription factor / Whirly transcription factor / Transcriptional Coactivator Pc4; Chain A / ssDNA-binding transcriptional regulator / Transcriptional Co-activator pc4; Chain A / Roll / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Single-stranded DNA-binding protein WHY2, mitochondrial
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.451 Å
AuthorsCappadocia, L. / Brisson, N. / Sygusch, J.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: A conserved lysine residue of plant Whirly proteins is necessary for higher order protein assembly and protection against DNA damage.
Authors: Cappadocia, L. / Parent, J.S. / Zampini, E. / Lepage, E. / Sygusch, J. / Brisson, N.
History
DepositionMar 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Why2 protein
B: DNA 32-mer dT32


Theoretical massNumber of molelcules
Total (without water)29,6322
Polymers29,6322
Non-polymers00
Water54030
1
A: Why2 protein
B: DNA 32-mer dT32

A: Why2 protein
B: DNA 32-mer dT32

A: Why2 protein
B: DNA 32-mer dT32

A: Why2 protein
B: DNA 32-mer dT32


Theoretical massNumber of molelcules
Total (without water)118,5278
Polymers118,5278
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-11
crystal symmetry operation21_655z+1,y,-x1
crystal symmetry operation23_554-z,y,x-11
Buried area16820 Å2
ΔGint-159 kcal/mol
Surface area33800 Å2
MethodPISA
2
A: Why2 protein
B: DNA 32-mer dT32
x 24


Theoretical massNumber of molelcules
Total (without water)711,16448
Polymers711,16448
Non-polymers00
Water86548
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_654-x+1,y,-z-11
crystal symmetry operation4_564x,-y+1,-z-11
crystal symmetry operation5_654z+1,x,y-11
crystal symmetry operation6_665z+1,-x+1,-y1
crystal symmetry operation7_564-z,-x+1,y-11
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_564y,z+1,x-11
crystal symmetry operation10_665-y+1,z+1,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_654-y+1,-z,x-11
crystal symmetry operation13_554y,x,-z-11
crystal symmetry operation14_664-y+1,-x+1,-z-11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_565x,z+1,-y1
crystal symmetry operation18_664-x+1,z+1,y-11
crystal symmetry operation19_655-x+1,-z,-y1
crystal symmetry operation20_554x,-z,y-11
crystal symmetry operation21_655z+1,y,-x1
crystal symmetry operation22_664z+1,-y+1,x-11
crystal symmetry operation23_554-z,y,x-11
crystal symmetry operation24_565-z,-y+1,-x1
Buried area128320 Å2
ΔGint-982 kcal/mol
Surface area175390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.465, 166.465, 166.465
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
DetailsAuthors state that the biological unit is a tetramer protein plus a 32-mer DNA molecule, as indicated as pentamer in remark 350. Please refer to remark 999 for more details on the sequences specificity of this crystal structure.

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Components

#1: Protein Why2 protein


Mass: 19942.613 Da / Num. of mol.: 1 / Fragment: Residues 48-216 / Mutation: K67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Strain: kennebec / Gene: StWhy2 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D9J034
#2: DNA chain DNA 32-mer dT32


Mass: 9689.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesis
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THE CRYSTALLIZED DNA IS A 32-MER OLIGONUCLEOTIDE WITH SEQUENCE ...THE SEQUENCE OF THE CRYSTALLIZED DNA IS A 32-MER OLIGONUCLEOTIDE WITH SEQUENCE TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT. ONLY 9 RESIDUES WERE MODELED IN THE COORDINATES OF THE ASYMMETRIC UNIT. ACCORDING TO THE AUTHORS, THE 32-MER DNA BINDS A TETRAMER THAT INCLUDE FOUR MONOMERS OF FOUR ASYMMETRIC UNITS; THE STWHY2-DNA BINDING IS NOT SEQUENCE SPECIFIC THUS EACH TETRAMERIC PROTEIN BINDS A 32-MER DNA IN DIFFERENT SEQUENCE REGISTERS; AS A RESULT ONLY THREE OF THE FOUR DNA-BINDING SITES OF EACH TETRAMER WOULD BE PHYSICALLY OCCUPIED BY THE DNA.

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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: 2.14 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris pH8.0, 15% PEG6000, 1200mM LiCl, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2008
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 7712 / Num. obs: 7685 / % possible obs: 99.65 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.6 % / Biso Wilson estimate: 67.51 Å2 / Rsym value: 0.067 / Net I/σ(I): 24.5

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3N1J

3n1j


Resolution: 2.451→29.427 Å / Occupancy max: 1 / Occupancy min: 0.74 / FOM work R set: 0.7179 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 595 7.89 %RANDOM
Rwork0.2498 ---
obs0.2514 7540 97.77 %-
all-7712 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.801 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 109.49 Å2 / Biso mean: 68.9694 Å2 / Biso min: 45.41 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.451→29.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 180 0 30 1472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031491
X-RAY DIFFRACTIONf_angle_d0.7052052
X-RAY DIFFRACTIONf_chiral_restr0.04225
X-RAY DIFFRACTIONf_plane_restr0.002236
X-RAY DIFFRACTIONf_dihedral_angle_d16.718557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4512-2.69770.41571320.37241590172293
2.6977-3.08770.41171230.31041733185698
3.0877-3.88880.27331700.240217351905100
3.8888-29.42920.23141700.229618872057100

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