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- PDB-3n1j: Crystal structure of a StWhy2-dT32 complex -

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Basic information

Entry
Database: PDB / ID: 3n1j
TitleCrystal structure of a StWhy2-dT32 complex
Components
  • DNA 32-mer dT32
  • Protein StWhy2
KeywordsDNA BINDING PROTEIN/DNA / Single-stranded DNA binding protein / Plant / Whirly / Protein-DNA complex / 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 / Single-stranded DNA-binding protein WHY2, mitochondrial
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsCappadocia, L. / Brisson, N. / Sygusch, J.
CitationJournal: Plant Cell / Year: 2010
Title: Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair.
Authors: Cappadocia, L. / Marechal, A. / Parent, J.S. / Lepage, E. / Sygusch, J. / Brisson, N.
History
DepositionMay 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein StWhy2
B: DNA 32-mer dT32


Theoretical massNumber of molelcules
Total (without water)22,6932
Polymers22,6932
Non-polymers00
Water1,08160
1
A: Protein StWhy2
B: DNA 32-mer dT32
x 24


Theoretical massNumber of molelcules
Total (without water)544,64448
Polymers544,64448
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 area128240 Å2
ΔGint-985 kcal/mol
Surface area171920 Å2
MethodPISA
2
A: Protein StWhy2
B: DNA 32-mer dT32

A: Protein StWhy2
B: DNA 32-mer dT32

A: Protein StWhy2
B: DNA 32-mer dT32

A: Protein StWhy2
B: DNA 32-mer dT32


Theoretical massNumber of molelcules
Total (without water)90,7748
Polymers90,7748
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
Unit cell
Length a, b, c (Å)166.495, 166.495, 166.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 Protein StWhy2


Mass: 20000.715 Da / Num. of mol.: 1
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*PLUS
#2: DNA chain DNA 32-mer dT32


Mass: 2692.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Synthesis
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 25% PEG6000, 0.1M Tris, 1.2M LiCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 6196 / Num. obs: 6188 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.1 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.118 / Net I/σ(I): 9.1
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 605 / Rsym value: 0.87 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
PHENIXmodel building
CNSrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L3A

1l3a


Resolution: 2.65→38.197 Å / SU ML: 2.53 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 603 10.03 %RANDOM
Rwork0.2115 ---
obs0.216 6011 97.12 %-
all-6188 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.914 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso mean: 54.37 Å2
Baniso -1Baniso -2Baniso -3
1--3.1633 Å2-0 Å2-0 Å2
2---3.1633 Å20 Å2
3----3.1633 Å2
Refinement stepCycle: LAST / Resolution: 2.65→38.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 180 0 60 1506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061495
X-RAY DIFFRACTIONf_angle_d0.9972056
X-RAY DIFFRACTIONf_dihedral_angle_d18.387558
X-RAY DIFFRACTIONf_chiral_restr0.055225
X-RAY DIFFRACTIONf_plane_restr0.003236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.91640.31181390.26381234X-RAY DIFFRACTION92
2.9164-3.33820.2951450.21241317X-RAY DIFFRACTION97
3.3382-4.20490.22821540.17761376X-RAY DIFFRACTION100
4.2049-38.20050.24721650.21471481X-RAY DIFFRACTION99

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