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- PDB-1enh: STRUCTURAL STUDIES OF THE ENGRAILED HOMEODOMAIN -

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Basic information

Entry
Database: PDB / ID: 1enh
TitleSTRUCTURAL STUDIES OF THE ENGRAILED HOMEODOMAIN
ComponentsENGRAILED HOMEODOMAIN
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN
Function / homology
Function and homology information


posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation ...posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation / wing disc morphogenesis / neuroblast fate determination / imaginal disc-derived wing vein specification / segment polarity determination / ventral midline development / compartment pattern specification / gonad development / axon guidance / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of gene expression / sequence-specific DNA binding / negative regulation of neuron apoptotic process / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Homeobox domain engrailed / Homeobox engrailed, C-terminal / Homeobox engrailed-type, conserved site / Engrailed homeobox C-terminal signature domain / 'Homeobox' engrailed-type protein signature. / : / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. ...Homeobox domain engrailed / Homeobox engrailed, C-terminal / Homeobox engrailed-type, conserved site / Engrailed homeobox C-terminal signature domain / 'Homeobox' engrailed-type protein signature. / : / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / 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
Segmentation polarity homeobox protein engrailed
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsClarke, N.D. / Kissinger, C.R. / Desjarlais, J. / Gilliland, G.L. / Pabo, C.O.
Citation
Journal: Protein Sci. / Year: 1994
Title: Structural studies of the engrailed homeodomain.
Authors: Clarke, N.D. / Kissinger, C.R. / Desjarlais, J. / Gilliland, G.L. / Pabo, C.O.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1990
Title: Crystal Structure of an Engrailed Homeodomain-DNA Complex at 2.8 Resolution: A Framework for Understanding Homeodomain-DNA Interactions
Authors: Kissinger, C.R. / Liu, B. / Martin-Blanco, E. / Kornberg, T.B. / Pabo, C.O.
History
DepositionMay 20, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENGRAILED HOMEODOMAIN


Theoretical massNumber of molelcules
Total (without water)6,6201
Polymers6,6201
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.670, 44.670, 118.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein ENGRAILED HOMEODOMAIN


Mass: 6619.536 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / References: UniProt: P02836
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion, hanging drop
Details: referred to 'Liu B.', (1990) 'Biochem. Biophys. Res. Commun.', 171, 257-259
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14.5 mg/mlprotein1drop
330 mMbis-Tris-HCl1drop
474 %satammonium phosphate1reservoir
2DNA1dropduplex

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.89 Å / Num. obs: 6104 / % possible obs: 86.8 % / Num. measured all: 21567 / Rmerge(I) obs: 0.0375

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.197 -
obs0.197 4060
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms466 0 0 33 499
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.09
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197 / Highest resolution: 2.1 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.59
X-RAY DIFFRACTIONx_dihedral_angle_d1.18
X-RAY DIFFRACTIONx_dihedral_angle_deg

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