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- PDB-1m7u: Crystal structure of a novel DNA-binding domain from Ndt80, a tra... -

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Basic information

Entry
Database: PDB / ID: 1m7u
TitleCrystal structure of a novel DNA-binding domain from Ndt80, a transcriptional activator required for meiosis in yeast
ComponentsNdt80 protein
KeywordsTRANSCRIPTION ACTIVATOR / yeast protein / DNA-binding / meiosis
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
Meiosis-specific transcription factor NDT80
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.8 Å
AuthorsMontano, S.P. / Cote, M.L. / Fingerman, I. / Pierce, M. / Vershon, A.K. / Georgiadis, M.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal structure of the DNA-binding domain from Ndt80, a transcriptional activator required for meiosis in yeast
Authors: Montano, S.P. / Cote, M.L. / Fingerman, I. / Pierce, M. / Vershon, A.K. / Georgiadis, M.M.
History
DepositionJul 22, 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
Remark 999SEQUENCE THE DISCREPANCIES ARE PRESENT DUE TO ERRORS IN PCR.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ndt80 protein
B: Ndt80 protein


Theoretical massNumber of molelcules
Total (without water)62,6152
Polymers62,6152
Non-polymers00
Water82946
1
A: Ndt80 protein


Theoretical massNumber of molelcules
Total (without water)31,3071
Polymers31,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ndt80 protein


Theoretical massNumber of molelcules
Total (without water)31,3071
Polymers31,3071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.960, 63.960, 285.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ndt80 protein


Mass: 31307.455 Da / Num. of mol.: 2 / Fragment: DNA binding domain, residues 59-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Ndt80 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon+ / References: UniProt: P38830
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulfate, citric acid, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 294 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.6 Mammonium sulfate1drop
20.1 Msodium citrate1droppH5.6
350 mMHEPES1droppH7.0
40.2 M1dropNaCl
51.6 Mammonium sulfate1reservoirpH5.6
6sodium citrate1reservoir

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jun 29, 2001
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 17541 / Num. obs: 17150 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 39 Å2 / Rsym value: 0.067 / Net I/σ(I): 18.6
Reflection shellResolution: 2.8→2.86 Å / Mean I/σ(I) obs: 6.8 / Rsym value: 0.21 / % possible all: 89.9
Reflection
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Lowest resolution: 2.9 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 6.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflectionSelection details
Rfree0.29 885 RANDOM
Rwork0.232 --
all-17541 -
obs-17150 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 0 0 46 3793
LS refinement shellResolution: 2.8→2.86 Å /
RfactorNum. reflection
Rfree0.37 60
Rwork0.32 -
obs-955
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.43
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / Rfactor Rwork: 0.32

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