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- PDB-1k61: MATALPHA2 HOMEODOMAIN BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1k61
TitleMATALPHA2 HOMEODOMAIN BOUND TO DNA
Components
  • 5'-D(*(5IU)P*GP*CP*GP*TP*GP*TP*AP*AP*AP*TP*GP*AP*AP*TP*TP*AP*CP*AP*TP*G)-3'
  • 5'-D(*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*CP*AP*TP*TP*TP*AP*CP*AP*CP*GP*C)-3'
  • Mating-type protein alpha-2
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / HOMEODOMAIN / HOOGSTEEN BASE PAIR / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


: / regulation of mating-type specific transcription, DNA-templated / RNA polymerase II transcription repressor complex / DNA binding, bending / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Mating-type protein ALPHA2 / Mating-type protein ALPHA2
Similarity search - Component
MethodX-RAY DIFFRACTION / MIR, molecular replacement / Resolution: 2.1 Å
AuthorsAishima, J. / Gitti, R.K. / Noah, J.E. / Gan, H.H. / Schlick, T. / Wolberger, C.
CitationJournal: NUCLEIC ACIDS RES. / Year: 2002
Title: A Hoogsteen base pair embedded in undistorted B-DNA
Authors: Aishima, J. / Gitti, R.K. / Noah, J.E. / Gan, H.H. / Schlick, T. / Wolberger, C.
History
DepositionOct 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: 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 / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-D(*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*CP*AP*TP*TP*TP*AP*CP*AP*CP*GP*C)-3'
F: 5'-D(*(5IU)P*GP*CP*GP*TP*GP*TP*AP*AP*AP*TP*GP*AP*AP*TP*TP*AP*CP*AP*TP*G)-3'
A: Mating-type protein alpha-2
B: Mating-type protein alpha-2
C: Mating-type protein alpha-2
D: Mating-type protein alpha-2


Theoretical massNumber of molelcules
Total (without water)42,0966
Polymers42,0966
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.940, 70.240, 68.290
Angle α, β, γ (deg.)90.00, 105.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 5'-D(*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*CP*AP*TP*TP*TP*AP*CP*AP*CP*GP*C)-3'


Mass: 6381.160 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence is derived from the STE6 promoter region, with the MCM1 binding sites removed.
#2: DNA chain 5'-D(*(5IU)P*GP*CP*GP*TP*GP*TP*AP*AP*AP*TP*GP*AP*AP*TP*TP*AP*CP*AP*TP*G)-3'


Mass: 6613.103 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence is derived from the STE6 promoter region, with the MCM1 binding sites removed.
#3: Protein
Mating-type protein alpha-2 / Alpha-2 repressor


Mass: 7275.384 Da / Num. of mol.: 4 / Fragment: RESIDUES 132-191, HOMEODOMAIN / Source method: obtained synthetically
Details: The sequence naturally occurs in yeast. The protein was synthesized by the FMOC method.
References: UniProt: P01367, UniProt: P0CY08*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 6000, Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2Bicine11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 24, 1998 / Details: Yale 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→16 Å / Num. all: 23364 / Num. obs: 23014 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.07 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 14
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2897 / % possible all: 81
Reflection
*PLUS
Lowest resolution: 16 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MIR, molecular replacement
Starting model: PDB ENTRY 1APL

1apl


Resolution: 2.1→16.01 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 23852424.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: Refinement Target values for the DNA as described in: G.Parkinson, J.Vojtechovsky, L.Clowney, A.T.Brunger, H.M.Berman, New Parameters for the Refinement of Nucleic Acid Containing ...Details: Refinement Target values for the DNA as described in: G.Parkinson, J.Vojtechovsky, L.Clowney, A.T.Brunger, H.M.Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996). Modified for 5-iodouracil residue.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1976 9.8 %RANDOM
Rwork0.221 ---
obs0.221 20065 96.6 %-
all-20799 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.8193 Å2 / ksol: 0.327842 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.33 Å20 Å24.57 Å2
2---1.09 Å20 Å2
3----6.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-20 Å
Luzzati sigma a0.33 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→16.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 854 1 195 2961
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 312 9.7 %
Rwork0.26 2921 -
obs--93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2I_DNA-RNA.PARAMI_DNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.1 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11

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