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- PDB-3hdd: ENGRAILED HOMEODOMAIN DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 3hdd
TitleENGRAILED HOMEODOMAIN DNA COMPLEX
Components
  • 5'-D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3'
  • 5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*TP*AP*CP*CP*TP*AP*A)-3'
  • ENGRAILED HOMEODOMAIN
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 / Resolution: 2.2 Å
AuthorsFraenkel, E. / Rould, M.A. / Chambers, K.A. / Pabo, C.O.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures.
Authors: Fraenkel, E. / Rould, M.A. / Chambers, K.A. / Pabo, C.O.
History
DepositionJul 13, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
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
C: 5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*TP*AP*CP*CP*TP*AP*A)-3'
D: 5'-D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3'
A: ENGRAILED HOMEODOMAIN
B: ENGRAILED HOMEODOMAIN


Theoretical massNumber of molelcules
Total (without water)27,5304
Polymers27,5304
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.620, 45.520, 72.930
Angle α, β, γ (deg.)90.00, 118.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 6387.157 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN / Source method: obtained synthetically
Details: HOMEODOMAIN SEQUENCE FROM DROSOPHILA MELANOGASTER (FRUIT FLY)
#2: DNA chain 5'-D(*AP*TP*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3'


Mass: 6494.248 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN / Source method: obtained synthetically
Details: HOMEODOMAIN SEQUENCE FROM DROSOPHILA MELANOGASTER (FRUIT FLY)
#3: Protein ENGRAILED HOMEODOMAIN


Mass: 7324.371 Da / Num. of mol.: 2
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.: 53 / 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: 3.41 Å3/Da / Density % sol: 48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: COMPLEX WAS CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION OVER 0.26M AMOAC AND 1% PEG400., pH 7.0, vapor diffusion - hanging drop
Components of the solutions
IDNameCrystal-IDSol-ID
1AMOAC11
2PEG 40011
3PEG 40012
Crystal
*PLUS
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMprotein1drop
21 Mammonium acetate1drop
31 %(v/v)PEG4001reservoir
40.25 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 15, 1995 / Details: MIRRORS
RadiationMonochromator: NI MIRROR AND NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 18176 / % possible obs: 94 % / Redundancy: 2.6 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 25
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4 / % possible all: 70
Reflection
*PLUS
Num. measured all: 47760
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 70 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementStarting model: PDB ENTRY 1HDD

1hdd


Resolution: 2.2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1760 10 %RANDOM
Rwork0.204 ---
obs0.204 17663 93.7 %-
all-17663 --
Displacement parametersBiso mean: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.66 Å2
2--0.11 Å20 Å2
3---0.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 855 0 53 1864
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.111.5
X-RAY DIFFRACTIONx_mcangle_it3.522
X-RAY DIFFRACTIONx_scbond_it3.892
X-RAY DIFFRACTIONx_scangle_it6.472.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 198 9 %
Rwork0.35 2002 -
obs--75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARNDBX.DNATOPNDBX.DNA
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21
LS refinement shell
*PLUS
Rfactor Rwork: 0.35

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