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- PDB-2evh: Structure of a Ndt80-DNA complex (MSE mutant mA7G) -

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Basic information

Entry
Database: PDB / ID: 2evh
TitleStructure of a Ndt80-DNA complex (MSE mutant mA7G)
Components
  • 5'-D(*AP*GP*TP*TP*TP*CP*TP*GP*TP*GP*TP*CP*GP*C)-3'
  • 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*GP*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: 1.989 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 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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 1.5Aug 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*GP*AP*CP*AP*CP*AP*GP*AP*AP*AP*C)-3'
C: 5'-D(*AP*GP*TP*TP*TP*CP*TP*GP*TP*GP*TP*CP*GP*C)-3'
A: NDT80 protein


Theoretical massNumber of molelcules
Total (without water)48,1513
Polymers48,1513
Non-polymers00
Water5,405300
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.534, 78.441, 161.334
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*GP*AP*CP*AP*CP*AP*GP*AP*AP*AP*C)-3'


Mass: 4282.820 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*CP*TP*GP*TP*GP*TP*CP*GP*C)-3'


Mass: 4277.774 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.: 300 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
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 5 mM DTT. 1:1 Molar ratio protein:DNA, protein at 15 mg/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: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0093 Å
DetectorType: SBC-2 / Detector: CCD / Date: Dec 8, 2001
RadiationMonochromator: Rosenbaum-Rock monochromator #1 high-resolution double-crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 1.989→43.8 Å / Num. all: 29735 / Num. obs: 29735 / % possible obs: 97.23 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.989→2.12 Å / % possible all: 93.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
HKL-2000data 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: 1.989→43.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.405 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1508 5 %RANDOM
Rwork0.179 ---
all0.18 29873 --
obs0.18 29873 97.23 %-
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: 19.278 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.989→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 551 0 300 3252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213072
X-RAY DIFFRACTIONr_bond_other_d0.0020.022485
X-RAY DIFFRACTIONr_angle_refined_deg1.3312.1874278
X-RAY DIFFRACTIONr_angle_other_deg1.12135860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6565287
X-RAY DIFFRACTIONr_chiral_restr0.0750.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022945
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02503
X-RAY DIFFRACTIONr_nbd_refined0.1790.3487
X-RAY DIFFRACTIONr_nbd_other0.2360.32941
X-RAY DIFFRACTIONr_nbtor_other0.0860.51686
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.5405
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.35
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.339
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3690.520
X-RAY DIFFRACTIONr_mcbond_it0.6781.51467
X-RAY DIFFRACTIONr_mcangle_it1.24222416
X-RAY DIFFRACTIONr_scbond_it1.40231605
X-RAY DIFFRACTIONr_scangle_it2.1924.51862
LS refinement shellResolution: 1.989→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.289 72
Rwork0.248 1632
obs-1704

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