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- PDB-8ton: Crystal Structure of Engineered Mouse Protocadherin-15 EC3-EC7 Co... -

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Basic information

Entry
Database: PDB / ID: 8ton
TitleCrystal Structure of Engineered Mouse Protocadherin-15 EC3-EC7 Connection
ComponentsProtocadherin-15 EC3-EC7
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


detection of mechanical stimulus involved in equilibrioception / detection of mechanical stimulus involved in sensory perception of sound / inner ear receptor cell stereocilium organization / righting reflex / inner ear auditory receptor cell differentiation / stereocilium / non-motile cilium assembly / auditory receptor cell stereocilium organization / adult walking behavior / homophilic cell adhesion via plasma membrane adhesion molecules ...detection of mechanical stimulus involved in equilibrioception / detection of mechanical stimulus involved in sensory perception of sound / inner ear receptor cell stereocilium organization / righting reflex / inner ear auditory receptor cell differentiation / stereocilium / non-motile cilium assembly / auditory receptor cell stereocilium organization / adult walking behavior / homophilic cell adhesion via plasma membrane adhesion molecules / startle response / inner ear development / photoreceptor outer segment / visual perception / actin filament organization / morphogenesis of an epithelium / locomotory behavior / sensory perception of sound / multicellular organism growth / response to calcium ion / cell adhesion / calcium ion binding / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
: / Protocadherin-15
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsDe-la-Torre, P. / Brower, J. / Indzhykulian, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01 DC020190 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01 DC017166 United States
CitationJournal: To Be Published
Title: Crystal Structure of Engineered Mouse Protocadherin-15 EC3-EC7 Connection
Authors: De-la-Torre, P. / Brower, J. / Indzhykulian, A.
History
DepositionAug 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protocadherin-15 EC3-EC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0964
Polymers27,9931
Non-polymers1023
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.603, 84.603, 76.895
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

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Components

#1: Protein Protocadherin-15 EC3-EC7


Mass: 27993.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Expressed with Rosetta (DE3) competent cells / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdh15 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q99PJ1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% w/v PEG 20000, 0.1 M Tris HCl pH 8.5, 0.6 uM Spermine Tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 A
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 23952 / % possible obs: 99.9 % / Redundancy: 11.6 % / CC1/2: 1 / CC star: 1 / Net I/σ(I): 31.9285
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 1.86 / Num. unique obs: 1173 / CC1/2: 0.728 / CC star: 0.918 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→42.34 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.382 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2234 1201 5.024 %
Rwork0.1839 22704 -
all0.186 --
obs-23905 99.929 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.309 Å2-0.154 Å2-0 Å2
2---0.309 Å20 Å2
3---1.002 Å2
Refinement stepCycle: LAST / Resolution: 1.94→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 3 125 1904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121828
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161702
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.6612504
X-RAY DIFFRACTIONr_angle_other_deg0.5731.573924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.055224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.212512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14710279
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.8431093
X-RAY DIFFRACTIONr_chiral_restr0.0880.2285
X-RAY DIFFRACTIONr_chiral_restr_other0.0180.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02407
X-RAY DIFFRACTIONr_nbd_refined0.2390.2285
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.21543
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2887
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21007
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2102
X-RAY DIFFRACTIONr_metal_ion_refined0.3060.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1060.24
X-RAY DIFFRACTIONr_nbd_other0.1920.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.25
X-RAY DIFFRACTIONr_mcbond_it4.584.179896
X-RAY DIFFRACTIONr_mcbond_other4.5774.178896
X-RAY DIFFRACTIONr_mcangle_it5.6417.4641117
X-RAY DIFFRACTIONr_mcangle_other5.6397.4711118
X-RAY DIFFRACTIONr_scbond_it6.3884.832932
X-RAY DIFFRACTIONr_scbond_other6.3664.828931
X-RAY DIFFRACTIONr_scangle_it9.0438.5611386
X-RAY DIFFRACTIONr_scangle_other9.048.5651387
X-RAY DIFFRACTIONr_lrange_it10.52852.7527507
X-RAY DIFFRACTIONr_lrange_other10.54152.6957420
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.941-1.9910.33810.32516410.32517220.930.9311000.347
1.991-2.0460.293850.25416270.25617120.9490.9551000.272
2.046-2.1050.203780.20815630.20816410.9740.971000.221
2.105-2.1690.233600.19815620.19916220.9610.9741000.214
2.169-2.240.209860.20714660.20715520.9710.9721000.227
2.24-2.3190.301700.19314260.19814960.9390.9771000.21
2.319-2.4060.228750.17813970.18114730.9630.98199.93210.196
2.406-2.5040.236650.16613340.16813990.9720.9831000.182
2.504-2.6150.267660.16712760.17113420.9540.9831000.188
2.615-2.7420.23700.18412330.18613030.9670.9781000.204
2.742-2.8890.206650.211670.212330.9740.97599.91890.223
2.889-3.0640.278750.22110900.22411660.9580.9799.91420.252
3.064-3.2740.299510.22410590.22711100.9440.9711000.258
3.274-3.5350.254620.2189770.2210390.9590.9761000.247
3.535-3.8690.233520.1869000.1899540.9690.9899.79040.221
3.869-4.3220.274460.1498100.1548570.9620.98799.88330.189
4.322-4.9820.115450.1317340.137790.9910.991000.179
4.982-6.080.233240.1526400.1556650.9820.98999.84960.197
6.08-8.5110.207280.1684970.175300.9820.98599.05660.225
8.511-42.3370.107170.1713050.1683240.9910.97999.38270.216

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