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- PDB-2evf: Structure of a Ndt80-DNA complex (MSE mutant mA6T) -

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Basic information

Entry
Database: PDB / ID: 2evf
TitleStructure of a Ndt80-DNA complex (MSE mutant mA6T)
Components
  • 5'-D(*AP*GP*TP*TP*TP*TP*AP*GP*TP*GP*TP*CP*GP*C)-3'
  • 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*TP*AP*AP*AP*AP*C)-3'
  • NDT80 protein
KeywordsCELL CYCLE/DNA / BETA-BARREL / IG-FOLD TRANSCRIPTION FACTOR / 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: 1.56 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 31, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,1503
Polymers48,1503
Non-polymers00
Water7,656425
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.193, 78.754, 161.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-664-

HOH

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Components

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


Mass: 4257.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MUTANT MSE DNA STRAND 1
#2: DNA chain 5'-D(*AP*GP*TP*TP*TP*TP*AP*GP*TP*GP*TP*CP*GP*C)-3'


Mass: 4301.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MUTANT MSE DNA STRAND 2
#3: Protein NDT80 protein


Mass: 39590.527 Da / Num. of mol.: 1 / Fragment: NDT80 DNA BINDING DOMAIN / Mutation: s146g, i200t
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.: 425 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG 400, 50 mM bis-tris-propane pH 7.0, 100 mM NaCl, 50 mM CaCl2, and 1 mM DTT. 1:1 Molar ratio protein:DNA, protein at 20mg/ml, 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 / Details: MIRROR
RadiationMonochromator: KOHZU: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072158 Å / Relative weight: 1
ReflectionResolution: 1.56→23.56 Å / Num. all: 63123 / Num. obs: 63123 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.56-1.643.20.2393.186090.23993.4
1.64-1.7440.143585970.14398.4
1.74-1.864.30.0937.181950.09399.6
1.86-2.014.60.0777.676870.07799.7
2.01-2.215.30.076870920.07699.9
2.21-2.476.70.0659.264070.065100
2.47-2.858.50.061056910.06100
2.85-3.498.80.04612.648650.046100
3.49-4.938.40.03716.338160.037100
4.93-23.567.60.03317.721640.03399.1

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB 1MNN - MINUS DNA AT SEQUENCE CHANGES AND 1 BASEPAIR ADJACENT TO THOSE CHANGES

1mnn


Resolution: 1.56→23.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.229 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3191 5.1 %RANDOM
Rwork0.172 ---
all0.173 63060 --
obs0.173 63060 98.65 %-
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: 17.392 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.56→23.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 551 0 425 3409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213103
X-RAY DIFFRACTIONr_bond_other_d0.0020.022512
X-RAY DIFFRACTIONr_angle_refined_deg1.4122.1854322
X-RAY DIFFRACTIONr_angle_other_deg0.89735931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.625289
X-RAY DIFFRACTIONr_chiral_restr0.080.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022972
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02510
X-RAY DIFFRACTIONr_nbd_refined0.1970.3474
X-RAY DIFFRACTIONr_nbd_other0.2370.33035
X-RAY DIFFRACTIONr_nbtor_other0.0860.51709
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.5539
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2790.345
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3280.528
X-RAY DIFFRACTIONr_mcbond_it1.42631479
X-RAY DIFFRACTIONr_mcangle_it2.46542444
X-RAY DIFFRACTIONr_scbond_it2.78351624
X-RAY DIFFRACTIONr_scangle_it4.189101878
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.292 225
Rwork0.247 4023
obs-4248

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