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- PDB-1ig7: Msx-1 Homeodomain/DNA Complex Structure -

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Basic information

Entry
Database: PDB / ID: 1ig7
TitleMsx-1 Homeodomain/DNA Complex Structure
Components
  • 5'-D(*CP*AP*CP*TP*AP*AP*TP*TP*GP*AP*AP*GP*G)-3'
  • 5'-D(P*TP*CP*CP*TP*TP*CP*AP*AP*TP*TP*AP*GP*TP*GP*AP*C)-3'
  • Homeotic protein Msx-1
KeywordsTRANSCRIPTION/DNA / helix-turn-helix / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


cell surface receptor signaling pathway involved in heart development / activation of meiosis / negative regulation of odontoblast differentiation / positive regulation of mesenchymal cell apoptotic process / embryonic nail plate morphogenesis / nose development / cartilage morphogenesis / regulation of odontogenesis / negative regulation of striated muscle cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation ...cell surface receptor signaling pathway involved in heart development / activation of meiosis / negative regulation of odontoblast differentiation / positive regulation of mesenchymal cell apoptotic process / embryonic nail plate morphogenesis / nose development / cartilage morphogenesis / regulation of odontogenesis / negative regulation of striated muscle cell differentiation / epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of odontogenesis / pituitary gland development / mesenchymal cell apoptotic process / mesenchymal cell proliferation / mammary gland epithelium development / positive regulation of BMP signaling pathway / bone morphogenesis / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / embryonic limb morphogenesis / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / face morphogenesis / odontogenesis / signal transduction involved in regulation of gene expression / anterior/posterior pattern specification / middle ear morphogenesis / embryonic digit morphogenesis / muscle organ development / midbrain development / forebrain development / odontogenesis of dentin-containing tooth / inner ear development / roof of mouth development / epithelial to mesenchymal transition / protein localization to nucleus / BMP signaling pathway / heart morphogenesis / cis-regulatory region sequence-specific DNA binding / positive regulation of cell cycle / nuclear periphery / RNA polymerase II transcription regulatory region sequence-specific DNA binding / stem cell differentiation / negative regulation of cell growth / cellular response to nicotine / DNA-binding transcription repressor activity, RNA polymerase II-specific / cell morphogenesis / p53 binding / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / in utero embryonic development / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / protein stabilization / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
: / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily ...: / 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) / Homeobox protein MSX-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHovde, S. / Abate-Shen, C. / Geiger, J.H.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal structure of the Msx-1 homeodomain/DNA complex
Authors: Hovde, S. / Abate-Shen, C. / Geiger, J.H.
History
DepositionApr 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*CP*AP*CP*TP*AP*AP*TP*TP*GP*AP*AP*GP*G)-3'
C: 5'-D(P*TP*CP*CP*TP*TP*CP*AP*AP*TP*TP*AP*GP*TP*GP*AP*C)-3'
A: Homeotic protein Msx-1


Theoretical massNumber of molelcules
Total (without water)15,7873
Polymers15,7873
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.600, 60.960, 82.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3999.636 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*TP*CP*CP*TP*TP*CP*AP*AP*TP*TP*AP*GP*TP*GP*AP*C)-3'


Mass: 4848.165 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Homeotic protein Msx-1


Mass: 6939.079 Da / Num. of mol.: 1 / Fragment: Homeodomain (157-233)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pDs56-Msx-1(157-233) / Production host: Escherichia coli (E. coli) / References: UniProt: P13297
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.34 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Sodium Acetate11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 %PEG40001reservoir
20.1 Msodium 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: May 20, 1997 / Details: Osmic confocal maxflux mirrors
RadiationMonochromator: 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→40 Å / Num. all: 130352 / Num. obs: 11914 / % possible obs: 98.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.542 / % possible all: 97.7
Reflection
*PLUS
Highest resolution: 2.15 Å / Num. obs: 11219
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.298

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Even-Skipped Homeodomain/DNA complex

Resolution: 2.2→21.25 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 412425.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 836 10.4 %RANDOM
Rwork0.205 ---
all0.2119 10391 --
obs0.205 8007 88.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.12 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1-18.91 Å20 Å20 Å2
2---5.33 Å20 Å2
3----13.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→21.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms476 590 0 153 1219
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.026
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d2.01
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.712
X-RAY DIFFRACTIONc_scbond_it1.492
X-RAY DIFFRACTIONc_scangle_it2.292.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 113 10.1 %
Rwork0.261 1004 -
obs--75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0192
X-RAY DIFFRACTIONc_angle_deg2.174
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.01

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