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- PDB-1mnn: Structure of the sporulation specific transcription factor Ndt80 ... -

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Basic information

Entry
Database: PDB / ID: 1mnn
TitleStructure of the sporulation specific transcription factor Ndt80 bound to DNA
Components
  • 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*TP*GP*TP*CP*GP*C)-3'
  • 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*AP*AP*AP*AP*C)-3'
  • NDT80 protein
KeywordsTRANSCRIPTION/DNA / IG FOLD / PROTEIN_DNA COMPLEX / TRANSCRIPTION-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 / MAD / Resolution: 1.4 Å
AuthorsLamoureux, J.S. / Stuart, D. / Tsang, R. / Wu, C. / Glover, J.N.
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.
History
DepositionSep 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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 These descrepancies exist and are allelic variation as this gene was cloned from a ...SEQUENCE These descrepancies exist and are allelic variation as this gene was cloned from a different strain of yeast than the deposited sequence

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


Theoretical massNumber of molelcules
Total (without water)47,7233
Polymers47,7233
Non-polymers00
Water6,161342
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.143, 78.887, 161.522
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*AP*AP*AP*AP*C)-3'


Mass: 4266.821 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*TP*GP*TP*CP*GP*C)-3'


Mass: 4292.785 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein NDT80 protein


Mass: 39163.121 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN (residues 1-340)
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 47.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 400, calcium chloride, sodium chloride, bis-tris propane, DTT, spermine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2CaCl211
3NaCl11
4bis-tris propane11
5DTT11
6spermine11
7CaCl212
8NaCl12
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
230 %PEG4001reservoir
350 mMBis-Tris-propane1reservoirpH7.0
4100 mM1reservoirNaCl
550 mM1reservoirCaCl2
61.5 mM1reservoir
71 mMdithiothreitol1reservoir
81

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98008 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 1, 2001
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98008 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. all: 88384 / Num. obs: 88384 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 38 % / Rsym value: 0.051 / Net I/σ(I): 35
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3 / Rsym value: 0.493 / % possible all: 97.8
Reflection
*PLUS
Lowest resolution: 100 Å / Redundancy: 38 % / Num. measured all: 3338673 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Highest resolution: 1.4 Å / % possible obs: 97.8 % / Rmerge(I) obs: 0.493

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5refinement
RefinementMethod to determine structure: MAD / Resolution: 1.4→81.65 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.283 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.06 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20636 4438 5 %RANDOM
Rwork0.19484 ---
all0.19544 83611 --
obs0.19544 83611 99.81 %-
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: 19.621 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.82 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.4→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 568 0 342 3240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213078
X-RAY DIFFRACTIONr_bond_other_d0.0010.022487
X-RAY DIFFRACTIONr_angle_refined_deg1.5152.1944283
X-RAY DIFFRACTIONr_angle_other_deg0.94835851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7133287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10715473
X-RAY DIFFRACTIONr_chiral_restr0.0980.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022934
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02493
X-RAY DIFFRACTIONr_nbd_refined0.2160.3510
X-RAY DIFFRACTIONr_nbd_other0.210.32499
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.5337
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1060.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.332
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.513
X-RAY DIFFRACTIONr_mcbond_it1.1321.51465
X-RAY DIFFRACTIONr_mcangle_it2.08122406
X-RAY DIFFRACTIONr_scbond_it2.22931608
X-RAY DIFFRACTIONr_scangle_it3.3594.51877
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.287 317
Rwork0.269 6037
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4854-0.2407-0.20070.39740.42310.4142-0.00980.03210.02540.0330.0009-0.00620.01170.04110.00890.05940.01880.00590.05260.00240.06072.854216.695664.2594
20.9401-0.3372-0.04290.9521-0.78580.9652-0.05650.22480.0647-0.02030.0134-0.1423-0.14660.43480.04310.036-0.04810.03630.21370.01840.066622.176219.45546.6611
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC33 - 33533 - 335
2X-RAY DIFFRACTION2BA1 - 141 - 14
3X-RAY DIFFRACTION2CB1 - 141 - 14
Refinement
*PLUS
Lowest resolution: 100 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.52
LS refinement shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.42 Å

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