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- PDB-1mn4: Structure of Ndt80 (Residues 59-340) DNA-binding domain core -

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Basic information

Entry
Database: PDB / ID: 1mn4
TitleStructure of Ndt80 (Residues 59-340) DNA-binding domain core
ComponentsNDT80 PROTEIN
KeywordsTRANSCRIPTION / IG FOLD / PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


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
Meiosis-specific transcription factor NDT80
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsLamoureux, J.S. / Stuart, D. / Tsang, R. / Wu, C. / Glover, J.N.M.
CitationJournal: Embo J. / Year: 2002
Title: Structure of the sporulation-specific transcription factor Ndt80 bound to DNA
Authors: Lamoureux, J.S. / Stuart, D. / Tsang, R. / Wu, C. / Glover, J.N.M.
History
DepositionSep 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NDT80 PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,3861
Polymers32,3861
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.880, 41.930, 164.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NDT80 PROTEIN


Mass: 32385.701 Da / Num. of mol.: 1 / Fragment: DNA-binding core (Residues 59-340)
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.91 Å3/Da / Density % sol: 35.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, sodium acetate, magnesium chloride, spermine, 20mer DNA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14 mg/mlprotein1drop
2600 mMsodium acetate1reservoir
32 mM1reservoirMgCl2
41 mMspermine1reservoir
525 %PEG40001reservoir
6100 mMsodium acetate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9563 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 21, 2002 / Details: bent cylindrical Si-mirror (Rh coating)
RadiationMonochromator: Si(111) double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9563 Å / Relative weight: 1
ReflectionResolution: 2.2→14.95 Å / Num. all: 12530 / Num. obs: 13292 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.076 / Net I/σ(I): 20.9
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 7.9 / Rsym value: 0.221 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 12292 / Num. measured all: 144249 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.221

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→14.95 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 626 -random
Rwork0.226 ---
all0.229 13291 --
obs0.229 13086 98.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.73 Å2-1.32 Å2-4.41 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 0 89 2078
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_mcbond_it1.8371.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it3.1772
X-RAY DIFFRACTIONc_scangle_it3.5242.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor all: 0.229 / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.226 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.28

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