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- PDB-2hdd: ENGRAILED HOMEODOMAIN Q50K VARIANT DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2hdd
TitleENGRAILED HOMEODOMAIN Q50K VARIANT DNA COMPLEX
Components
  • DNA (5'-D(*AP*TP*CP*CP*GP*GP*GP*GP*AP*TP*TP*AP*CP*AP*TP*GP*G P*CP*AP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*CP*CP*C P*CP*GP*GP*A)-3')
  • PROTEIN (ENGRAILED HOMEODOMAIN Q50K)
KeywordsTRANSCRIPTION/DNA / DNA BINDING / COMPLEX (DNA BINDING PROTEIN-DNA) / TRANSCRIPTION-DNA COMPLEX
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 / negative regulation of neuron apoptotic process / sequence-specific DNA binding / 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
DNA / DNA (> 10) / Segmentation polarity homeobox protein engrailed
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.9 Å
AuthorsTucker-Kellogg, L. / Rould, M.A. / Chambers, K.A. / Ades, S.E. / Sauer, R.T. / Pabo, C.O.
CitationJournal: Structure / Year: 1997
Title: Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity.
Authors: Tucker-Kellogg, L. / Rould, M.A. / Chambers, K.A. / Ades, S.E. / Sauer, R.T. / Pabo, C.O.
History
DepositionFeb 10, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*CP*CP*C P*CP*GP*GP*A)-3')
D: DNA (5'-D(*AP*TP*CP*CP*GP*GP*GP*GP*AP*TP*TP*AP*CP*AP*TP*GP*G P*CP*AP*AP*A)-3')
A: PROTEIN (ENGRAILED HOMEODOMAIN Q50K)
B: PROTEIN (ENGRAILED HOMEODOMAIN Q50K)


Theoretical massNumber of molelcules
Total (without water)27,7394
Polymers27,7394
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.720, 45.340, 72.470
Angle α, β, γ (deg.)90.00, 119.53, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.703806, -0.704302, 0.092822), (-0.706709, 0.707442, 0.009334), (-0.07224, -0.059029, -0.995639)
Vector: 18.45795, 8.83419, 93.71819)

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Components

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


Mass: 6389.133 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*TP*CP*CP*GP*GP*GP*GP*AP*TP*TP*AP*CP*AP*TP*GP*G P*CP*AP*AP*A)-3')


Mass: 6496.224 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (ENGRAILED HOMEODOMAIN Q50K)


Mass: 7426.592 Da / Num. of mol.: 2 / Mutation: Q50K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P02836
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.23 Å3/Da / Density % sol: 48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: COMPLEX WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION OVER .75M AMOAC AND 1% PEG400; DROP STARTS AT 1M AMOAC., pH 7.00, vapor diffusion - hanging drop
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2AMMONIUM ACETATE11
3PEG 40011
4WATER12
5PEG 40012
6AMMONIUM ACETATE12
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlcomplex1drop
21 Mammonium acetate1drop
30.73-0.80 Mammonium acetate1reservoir
41 %PEG4001reservoir
51
61

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI MIRROR + NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 27136 / % possible obs: 94 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.035 / Rsym value: 0.044
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.38 / % possible all: 84
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % possible obs: 94 % / Redundancy: 3.4 %
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / % possible obs: 94 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→6 Å / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.251 -10 %RANDOM
Rwork0.205 ---
obs0.205 27136 94 %-
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 855 0 183 1990
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.46
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
LS refinement shellResolution: 1.9→1.97 Å / % reflection Rfree: 10 % / Total num. of bins used: 10 / % reflection obs: 84 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARNDBX.DNATOPNDBX.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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