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- PDB-1xm9: Structure of the armadillo repeat domain of plakophilin 1 -

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Basic information

Entry
Database: PDB / ID: 1xm9
TitleStructure of the armadillo repeat domain of plakophilin 1
Componentsplakophilin 1
KeywordsCELL ADHESION / armadillo repeat
Function / homology
Function and homology information


desmosome maintenance / intermediate filament bundle assembly / negative regulation of mRNA catabolic process / intermediate filament binding / structural constituent of skin epidermis / positive regulation of cap-dependent translational initiation / Keratinization / ameloblast differentiation / desmosome assembly / transepithelial water transport ...desmosome maintenance / intermediate filament bundle assembly / negative regulation of mRNA catabolic process / intermediate filament binding / structural constituent of skin epidermis / positive regulation of cap-dependent translational initiation / Keratinization / ameloblast differentiation / desmosome assembly / transepithelial water transport / positive regulation of cell-cell adhesion / desmosome / nuclear stress granule / Formation of the cornified envelope / lamin binding / cornified envelope / Apoptotic cleavage of cell adhesion proteins / positive regulation of keratinocyte differentiation / positive regulation of protein localization to membrane / intermediate filament / ficolin-1-rich granule membrane / positive regulation of protein localization to plasma membrane / adherens junction / cell-cell adhesion / cytoplasmic stress granule / cell adhesion / cadherin binding / Neutrophil degranulation / positive regulation of gene expression / perinuclear region of cytoplasm / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Plakophilin/Delta catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsChoi, H.J. / Weis, W.I.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure of the armadillo repeat domain of plakophilin 1.
Authors: Choi, H.J. / Weis, W.I.
History
DepositionOct 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: plakophilin 1


Theoretical massNumber of molelcules
Total (without water)50,4891
Polymers50,4891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.355, 131.977, 142.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein plakophilin 1


Mass: 50489.098 Da / Num. of mol.: 1 / Fragment: Armadillo repeat domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKP1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q13835

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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: 2.66 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: PEG 3350, Tris-Cl, potassium formate, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2003
RadiationMonochromator: double crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→48 Å / Num. all: 14705 / Num. obs: 13069 / % possible obs: 89 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 48.7 Å2 / Rsym value: 0.055
Reflection shellResolution: 2.8→2.9 Å / % possible all: 73

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→29.92 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2496803.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.324 1142 10 %RANDOM
Rwork0.255 ---
obs0.255 11452 89.9 %-
all-12744 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.2814 Å2 / ksol: 0.287631 e/Å3
Displacement parametersBiso mean: 70.3 Å2
Baniso -1Baniso -2Baniso -3
1--20.68 Å20 Å20 Å2
2--40.15 Å20 Å2
3----19.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 0 0 0 3237
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_scangle_it2.562.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.441 134 9.6 %
Rwork0.377 1264 -
obs--66.8 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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