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- PDB-2hos: Phage-Selected Homeodomain Bound to Unmodified DNA -

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Basic information

Entry
Database: PDB / ID: 2hos
TitlePhage-Selected Homeodomain Bound to Unmodified DNA
Components
  • 5'-D(*AP*TP*CP*CP*GP*GP*GP*GP*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*CP*CP*CP*CP*GP*GP*A)-3'
  • Segmentation polarity homeobox protein engrailed
KeywordsTranscription/DNA / Homeodomain / Phage Display / 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 / RSC-type complex / RNA polymerase II transcription regulatory region sequence-specific DNA binding / axon guidance / neuron differentiation / 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. / Homeodomain ...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
3-METHYL-1,3-OXAZOLIDIN-2-ONE / DNA / DNA (> 10) / Segmentation polarity homeobox protein engrailed
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShokat, K.M. / Feldman, M.E. / Simon, M.D.
CitationJournal: Acs Chem.Biol. / Year: 2006
Title: Structure and properties of a re-engineered homeodomain protein-DNA interface.
Authors: Simon, M.D. / Feldman, M.E. / Rauh, D. / Maris, A.E. / Wemmer, D.E. / Shokat, K.M.
History
DepositionJul 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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*CP*CP*CP*CP*GP*GP*A)-3'
D: 5'-D(*AP*TP*CP*CP*GP*GP*GP*GP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP*AP*AP*A)-3'
A: Segmentation polarity homeobox protein engrailed
B: Segmentation polarity homeobox protein engrailed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3889
Polymers27,9184
Non-polymers4695
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.097, 45.025, 73.081
Angle α, β, γ (deg.)90.00, 118.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

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DNA chain , 2 types, 2 molecules CD

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


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


Mass: 6496.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Commercial Solid Phase Synthesis

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Protein , 1 types, 2 molecules AB

#3: Protein Segmentation polarity homeobox protein engrailed / Homeobox


Mass: 7516.522 Da / Num. of mol.: 2 / Fragment: ENGRAILED HOMEODOMAIN / Mutation: I45V,I47G,Q50K,K52M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: en / Plasmid: pMal-EnHDf / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02836

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Non-polymers , 3 types, 134 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-3MO / 3-METHYL-1,3-OXAZOLIDIN-2-ONE / 3-METHYL-2-OXAZOLIDINONE


Mass: 101.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 3.24 Å3/Da / Density % sol: 61.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Well: 20% PEG400, 100mM NH4OAc Drop: 0.5mM DNA Protein Complex, 0.55M NH4OAc, 3.5mM bis-Tris-Propane, 10% PEG-400, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG40011
2NH4OAc11
3H2O11
4NH4OAc12
5bis-Tris-Propane12
6PEG40012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 25, 2005 / Details: KOHZU: Double Crystal Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 28750 / % possible obs: 84.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.862.30.391133.7
1.86-1.942.80.409152.7
1.94-2.033.10.349173.2
2.03-2.133.50.245187.4
2.13-2.273.70.184196.3
2.27-2.4440.143199.8
2.44-2.694.10.0891100
2.69-3.084.10.0481100
3.08-3.8840.026199.4
3.88-503.90.023199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HDD

2hdd


Resolution: 1.9→32.48 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.198 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25693 1710 6.8 %RANDOM
Rwork0.22308 ---
obs0.22535 23285 86.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.351 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å2-0.01 Å2
2--0.4 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 855 31 129 1965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211977
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7022.5062829
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6135122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52222.20359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03415205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.711518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021217
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.2703
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21224
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2149
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.691.5598
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1322923
X-RAY DIFFRACTIONr_scbond_it1.72631853
X-RAY DIFFRACTIONr_scangle_it2.6674.51901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 83 -
Rwork0.359 966 -
obs--49.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4584-1.014-1.203512.64041.35686.33370.08020.0281-0.0139-0.94540.0106-0.8471-0.06080.2179-0.09070.0597-0.03140.1222-0.20440.0044-0.212717.01629.50732.771
24.3849-0.1014-1.900511.4431-1.43333.3347-0.093-0.0582-0.05420.21890.04180.22250.091500.0511-0.1067-0.01340.0047-0.2502-0.0152-0.2947-3.63420.29762.288
311.52852.1346-1.34770.4576-0.09720.53-0.2852-0.4113-0.8804-0.18220.1812-0.5553-0.08440.29850.10410.0264-0.143-0.07080.22350.03750.13725.18728.43547.857
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC5 - 608 - 63
2X-RAY DIFFRACTION2BD2 - 595 - 62
3X-RAY DIFFRACTION3CA1 - 211 - 21
4X-RAY DIFFRACTION3DB22 - 421 - 21

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