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- PDB-1apl: CRYSTAL STRUCTURE OF A MAT-ALPHA2 HOMEODOMAIN-OPERATOR COMPLEX SU... -

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Basic information

Entry
Database: PDB / ID: 1apl
TitleCRYSTAL STRUCTURE OF A MAT-ALPHA2 HOMEODOMAIN-OPERATOR COMPLEX SUGGESTS A GENERAL MODEL FOR HOMEODOMAIN-DNA INTERACTIONS
Components
  • DNA (5'-D(*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*CP*AP*TP*TP*TP*AP*C P*AP*CP*GP*C)-3')
  • DNA (5'-D(*TP*GP*CP*GP*TP*GP*TP*AP*AP*AP*TP*GP*AP*AP*TP*TP*A P*CP*AP*TP*G)-3')
  • PROTEIN (MAT-ALPHA2 HOMEODOMAIN)
KeywordsDNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / DNA BINDING PROTEIN-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 / Silenced mating-type protein ALPHA2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsWolberger, C. / Vershon, A.K. / Liu, B. / Johnson, A.D. / Pabo, C.O.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1991
Title: Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions.
Authors: Wolberger, C. / Vershon, A.K. / Liu, B. / Johnson, A.D. / Pabo, C.O.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Preliminary X-Ray Diffraction Studies of a MAT-Alpha2-DNA Complex
Authors: Wolberger, C. / Vershon, A.K. / Johnson, A.D. / Pabo, C.O.
History
DepositionOct 4, 1993Deposition site: BNL / Processing site: BNL
Revision 1.0Oct 21, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*CP*AP*TP*TP*TP*AP*C P*AP*CP*GP*C)-3')
B: DNA (5'-D(*TP*GP*CP*GP*TP*GP*TP*AP*AP*AP*TP*GP*AP*AP*TP*TP*A P*CP*AP*TP*G)-3')
C: PROTEIN (MAT-ALPHA2 HOMEODOMAIN)
D: PROTEIN (MAT-ALPHA2 HOMEODOMAIN)


Theoretical massNumber of molelcules
Total (without water)32,4294
Polymers32,4294
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.780, 39.930, 68.790
Angle α, β, γ (deg.)90.00, 97.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6381.160 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*GP*CP*GP*TP*GP*TP*AP*AP*AP*TP*GP*AP*AP*TP*TP*A P*CP*AP*TP*G)-3')


Mass: 6501.232 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (MAT-ALPHA2 HOMEODOMAIN)


Mass: 9773.306 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAT ALPHA2 RES. 128-210 / Plasmid: PAV56 / Gene (production host): MAT ALPHA2 RES. 128-210 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B2C0, UniProt: P0CY08*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5 / Details: pH 7.50, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 40011
3CACL211
4NACLSodium chloride11
5WATER12
6PEG 40012
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 217.11-13 1991
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1protein1drop
2DNA1drop
310 %PEG4001reservoir
475 mM1reservoirCaCl2
51
61

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.9 Å / Num. obs: 7334 / % possible obs: 90 % / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 2.65 Å / Num. obs: 7907 / Num. measured all: 18265 / Rmerge(I) obs: 0.075

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.7→8 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.226 -
obs0.226 6730
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms938 855 0 0 1793
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(I): 1 / Rfactor obs: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg3.6

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