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- PDB-3r9z: Crystal Structure of StWhy2 K67A (form II) -

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Basic information

Entry
Database: PDB / ID: 3r9z
TitleCrystal Structure of StWhy2 K67A (form II)
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: 1.755 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
Water3,765209
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 operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area10370 Å2
ΔGint-125 kcal/mol
Surface area30360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.584, 90.584, 50.933
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Why2 protein


Mass: 19942.613 Da / Num. of mol.: 1 / Fragment: StWhy2 / 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.: 209 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM MOPS pH7.0, 18% PEG1000, 100mM NH4H2PO4, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.29 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2008
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.29 Å / Relative weight: 1
ReflectionResolution: 1.755→50 Å / Num. all: 21767 / Num. obs: 20419 / % possible obs: 93.8071 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 28.71 Å2 / Rsym value: 0.048 / Net I/σ(I): 21.5

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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: 3N1H

3n1h


Resolution: 1.755→33.846 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8384 / SU ML: 0.22 / Isotropic thermal model: isotropic with tls / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 964 4.86 %RANDOM
Rwork0.1921 ---
obs0.1933 19830 91.1 %-
all-21767 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.614 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso max: 103.5 Å2 / Biso mean: 39.4593 Å2 / Biso min: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.4901 Å20 Å2-0 Å2
2--2.4901 Å20 Å2
3----4.9802 Å2
Refinement stepCycle: LAST / Resolution: 1.755→33.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 10 209 1439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071258
X-RAY DIFFRACTIONf_angle_d11701
X-RAY DIFFRACTIONf_chiral_restr0.066182
X-RAY DIFFRACTIONf_plane_restr0.004218
X-RAY DIFFRACTIONf_dihedral_angle_d12.457454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.755-1.84750.3232750.28221490156552
1.8475-1.96330.27891420.22592618276090
1.9633-2.11480.22661490.18912863301298
2.1148-2.32760.23771400.19142855299597
2.3276-2.66430.24271500.195329363086100
2.6643-3.35620.21610.187529653126100
3.3562-33.85190.1981470.18683139328699
Refinement TLS params.Method: refined / Origin x: 5.9519 Å / Origin y: 25.5371 Å / Origin z: 14.7982 Å
111213212223313233
T0.1409 Å20.0013 Å20.0075 Å2-0.1312 Å2-0.0558 Å2--0.1398 Å2
L2.6724 °2-0.7787 °20.4363 °2-1.4673 °2-0.3742 °2--1.6546 °2
S0.0378 Å °0.2087 Å °-0.2216 Å °-0.1365 Å °-0.0315 Å °0.1263 Å °0.1177 Å °0.0349 Å °-0.0101 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA53 - 214
2X-RAY DIFFRACTION1allA1 - 2
3X-RAY DIFFRACTION1allA1 - 389

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