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Basic information

Entry
Database: PDB / ID: 2etw
TitlePrinciples of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes
Components
  • 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*TP*GP*TP*GP*GP*C)-3'
  • 5'-D(*TP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*C)-3'
  • NDT80 protein
KeywordsCELL CYCLE/DNA / beta sandwich / Ig-fold / B-DNA / CELL CYCLE-DNA COMPLEX
Function / homology
Function and homology information


sporulation / nuclear chromosome / meiotic cell cycle / sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / positive regulation of transcription by RNA polymerase II
Similarity search - Function
NDT80 DNA-binding domain / : / NDT80 DNA-binding domain / NDT80 DNA-binding domain superfamily / NDT80 / PhoG like DNA-binding family / NDT80 DNA-binding domain profile. / p53-like transcription factor, DNA-binding / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Meiosis-specific transcription factor NDT80
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.67 Å
AuthorsLamoureux, J.S. / Glover, J.N.
CitationJournal: Structure / Year: 2006
Title: Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes.
Authors: Lamoureux, J.S. / Glover, J.N.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-D(*TP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*C)-3'
C: 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*TP*GP*TP*GP*GP*C)-3'
A: NDT80 protein


Theoretical massNumber of molelcules
Total (without water)48,1503
Polymers48,1503
Non-polymers00
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.299, 78.919, 161.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain 5'-D(*TP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*C)-3'


Mass: 4226.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: vG1C MSE DNA strand 1
#2: DNA chain 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*TP*GP*TP*GP*GP*C)-3'


Mass: 4332.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: vG1C MSE DNA strand 2
#3: Protein NDT80 protein


Mass: 39590.527 Da / Num. of mol.: 1 / Fragment: Ndt80 DNA-binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NDT80 / Plasmid: PGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P38830
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 400, 50 mM bis-tris-propane pH 7.0, 100 mM NaCl, 50 mM CaCl2, and 1 mM DTT. 10mg/ml protein 1:1 molar ration with duplex DNA , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2bis-tris-propane11
3NaCl11
4CaCl211
5DTT11
6H2O11
7PEG 40012
8NaCl12
9CaCl212

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.072158 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2003
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072158 Å / Relative weight: 1
ReflectionResolution: 1.67→23.57 Å / Num. all: 51821 / Num. obs: 51821 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 10.5
Reflection shellResolution: 1.67→1.76 Å / % possible obs: 98.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 3.8 / Num. measured obs: 7464 / Rsym value: 0.176 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1MNN.pdb without water molecules and DNA at position -1,1,2 of the MSE.

1mnn


Resolution: 1.67→23.57 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.594 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2636 5.1 %RANDOM
Rwork0.18 ---
all0.181 51767 --
obs0.181 51767 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.272 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.67→23.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 551 0 331 3376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213169
X-RAY DIFFRACTIONr_bond_other_d0.0030.022573
X-RAY DIFFRACTIONr_angle_refined_deg1.3772.1794415
X-RAY DIFFRACTIONr_angle_other_deg1.19636079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4615297
X-RAY DIFFRACTIONr_chiral_restr0.0810.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023042
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02515
X-RAY DIFFRACTIONr_nbd_refined0.1940.3474
X-RAY DIFFRACTIONr_nbd_other0.2370.33031
X-RAY DIFFRACTIONr_nbtor_other0.0860.51669
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.5436
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.343
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3140.521
X-RAY DIFFRACTIONr_mcbond_it0.8171.51517
X-RAY DIFFRACTIONr_mcangle_it1.5222512
X-RAY DIFFRACTIONr_scbond_it1.80431652
X-RAY DIFFRACTIONr_scangle_it2.7664.51902
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.245 194
Rwork0.219 3516
all-3710

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