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- PDB-1m6u: Crystal Structure of a Novel DNA-binding domain from Ndt80, a Tra... -

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Basic information

Entry
Database: PDB / ID: 1m6u
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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 17, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE DISCREPANCIES ARE PRESENT DUE TO ERRORS IN PCR.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ndt80 protein
B: Ndt80 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9996
Polymers62,6152
Non-polymers3844
Water1,982110
1
A: Ndt80 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5964
Polymers31,3071
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ndt80 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4042
Polymers31,3071
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Ndt80 protein
hetero molecules

A: Ndt80 protein
hetero molecules

B: Ndt80 protein
hetero molecules

B: Ndt80 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,99812
Polymers125,2304
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_645-x+1,y-1,-z1
Buried area7890 Å2
ΔGint-168 kcal/mol
Surface area48080 Å2
MethodPISA
4
A: Ndt80 protein
hetero molecules

B: Ndt80 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9996
Polymers62,6152
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area2560 Å2
ΔGint-71 kcal/mol
Surface area25430 Å2
MethodPISA
5
A: Ndt80 protein
hetero molecules

A: Ndt80 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1918
Polymers62,6152
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4040 Å2
ΔGint-139 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.275, 64.897, 92.419
Angle α, β, γ (deg.)90.00, 107.52, 90.00
Int Tables number5
Space group name H-MC121

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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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 46.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: lithium sulfate, citric acid, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Montano, S.P., (2002) Acta Crystallogr., D58, 2127.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.9 mMprotein1drop
21.85-1.9 Mlithium sulfate1reservoir
30.1 Msodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 16, 2001 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 25573 / Num. obs: 25573 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.13 / Net I/σ(I): 15.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2128 / % possible all: 84.9
Reflection
*PLUS
Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 84.9 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ndt80, pdb entry 1M7U

1m7u


Resolution: 2.3→19.96 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1239 -RANDOM
Rwork0.226 ---
all-25573 --
obs-24433 95.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4057 0 20 110 4187
LS refinement shellResolution: 2.3→2.33 Å /
RfactorNum. reflection
Rfree0.43 48
Rwork0.33 -
obs-769
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.37
LS refinement shell
*PLUS
Rfactor Rfree: 0.43 / Rfactor Rwork: 0.33

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