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- PDB-3r9y: Crystal Structure of StWhy2 K67A (form I) -

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Basic information

Entry
Database: PDB / ID: 3r9y
TitleCrystal Structure of StWhy2 K67A (form I)
ComponentsWhy2 protein
KeywordsDNA BINDING PROTEIN / StWhy2 / single-stranded DNA binding protein / Plant / Potato / Whirly / Mitochondria
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
PHOSPHATE ION / Single-stranded DNA-binding protein WHY2, mitochondrial
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Why2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1333
Polymers19,9431
Non-polymers1902
Water75742
1
A: Why2 protein
hetero molecules

A: Why2 protein
hetero molecules

A: Why2 protein
hetero molecules

A: Why2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,53012
Polymers79,7704
Non-polymers7608
Water724
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 area10340 Å2
ΔGint-122 kcal/mol
Surface area31230 Å2
MethodPISA
2
A: Why2 protein
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)483,18172
Polymers478,62324
Non-polymers4,55948
Water43224
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 area85690 Å2
ΔGint-735 kcal/mol
Surface area163740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.365, 168.365, 168.365
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432

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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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM MOPS pH7.0, 24% PEG1000, 100mM NH4H2PO4, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 19, 2010
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 9014 / Num. obs: 9012 / % possible obs: 99.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.3 % / Biso Wilson estimate: 56.34 Å2 / Rsym value: 0.059 / Net I/σ(I): 31
Reflection shell
Resolution (Å)Redundancy (%)Rsym valueDiffraction-ID% possible all
2.35-2.4818.61.0251100
7.43-5018.70.018199.5

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N1H

3n1h


Resolution: 2.35→38.626 Å / Occupancy max: 1 / Occupancy min: 0.8 / FOM work R set: 0.7776 / SU ML: 0.37 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2664 519 5.95 %RANDOM
Rwork0.2236 ---
obs0.2263 8721 96.77 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.075 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 109.83 Å2 / Biso mean: 60.8141 Å2 / Biso min: 32.94 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.35→38.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 10 42 1314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051302
X-RAY DIFFRACTIONf_angle_d0.8941762
X-RAY DIFFRACTIONf_chiral_restr0.062189
X-RAY DIFFRACTIONf_plane_restr0.003227
X-RAY DIFFRACTIONf_dihedral_angle_d14.731470
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 (%)
2.3502-2.58670.3661200.29741883200392
2.5867-2.96090.36571280.26191993212196
2.9609-3.72990.25941270.23672074220199
3.7299-38.63080.24091440.202322522396100

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