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- PDB-8umz: Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Co... -

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Basic information

Entry
Database: PDB / ID: 8umz
TitleCrystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection
ComponentsProtocadherin-15 EC4-EC7
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


detection of mechanical stimulus involved in equilibrioception / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / righting reflex / stereocilium bundle / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / non-motile cilium assembly / auditory receptor cell stereocilium organization / adult walking behavior ...detection of mechanical stimulus involved in equilibrioception / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / righting reflex / stereocilium bundle / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / non-motile cilium assembly / auditory receptor cell stereocilium organization / adult walking behavior / startle response / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / actin filament bundle assembly / photoreceptor outer segment / visual perception / actin filament organization / morphogenesis of an epithelium / locomotory behavior / sensory perception of sound / response to calcium ion / multicellular organism growth / calcium ion binding / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain ...: / PCDH15-like domain / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsDe-la-Torre, P. / Martinez-Perez, K. / Indzhykulian, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01DC020190 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 EC4-EC7 Connection
Authors: De-la-Torre, P. / Martinez-Perez, K. / Indzhykulian, A.
History
DepositionOct 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 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 EC4-EC7
B: Protocadherin-15 EC4-EC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,29014
Polymers51,8432
Non-polymers44712
Water4,720262
1
A: Protocadherin-15 EC4-EC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1457
Polymers25,9221
Non-polymers2236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protocadherin-15 EC4-EC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1457
Polymers25,9221
Non-polymers2236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.276, 50.613, 88.263
Angle α, β, γ (deg.)90.000, 94.008, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protocadherin-15 EC4-EC7


Mass: 25921.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.: 10 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Sodium cacodylate pH 6.5,40% v/v MPD,5% w/v PEG 8000

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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 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 54156 / % possible obs: 93.6 % / Redundancy: 2.8 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.052 / Rrim(I) all: 0.091 / Net I/σ(I): 10.956
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.293 / Num. unique obs: 2557 / CC1/2: 0.841 / CC star: 0.956 / Rpim(I) all: 0.277 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→49.2 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.203 / SU ML: 0.109 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.27354 2561 5.1 %
Rwork0.22276 48084 -
all0.225 --
obs0.22276 48084 92.93 %
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: 23.224 Å2
Baniso -1Baniso -2Baniso -3
1--0.941 Å2-0 Å2-0.434 Å2
2---1.055 Å2-0 Å2
3---2.037 Å2
Refinement stepCycle: LAST / Resolution: 1.63→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 12 262 3782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123639
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163367
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.6674997
X-RAY DIFFRACTIONr_angle_other_deg0.5791.5667751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2855459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.068520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89810569
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.83210183
X-RAY DIFFRACTIONr_chiral_restr0.0840.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02824
X-RAY DIFFRACTIONr_nbd_refined0.2410.2649
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.23162
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21763
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21985
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2218
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.247
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2670.224
X-RAY DIFFRACTIONr_nbd_other0.2450.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.220
X-RAY DIFFRACTIONr_mcbond_it2.5452.3021797
X-RAY DIFFRACTIONr_mcbond_other2.5162.3021797
X-RAY DIFFRACTIONr_mcangle_it3.2264.1272248
X-RAY DIFFRACTIONr_mcangle_other3.2254.1282249
X-RAY DIFFRACTIONr_scbond_it3.3312.6181842
X-RAY DIFFRACTIONr_scbond_other3.3312.6181841
X-RAY DIFFRACTIONr_scangle_it4.6554.6792742
X-RAY DIFFRACTIONr_scangle_other4.6554.6792743
X-RAY DIFFRACTIONr_lrange_it5.53326.6233969
X-RAY DIFFRACTIONr_lrange_other5.5125.9763910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.6710.371560.293347X-RAY DIFFRACTION88.04
1.671-1.7170.322020.2673605X-RAY DIFFRACTION97.6655
1.717-1.7660.3131900.253523X-RAY DIFFRACTION97.5565
1.766-1.8210.3051980.233406X-RAY DIFFRACTION97.7223
1.821-1.880.2791510.2183230X-RAY DIFFRACTION94.2833
1.88-1.9460.2861530.2313235X-RAY DIFFRACTION97.9191
1.946-2.020.2791540.2213070X-RAY DIFFRACTION96.8168
2.02-2.1020.2851840.2252922X-RAY DIFFRACTION96.34
2.102-2.1950.271850.2222737X-RAY DIFFRACTION95.1792
2.195-2.3020.3051420.2242657X-RAY DIFFRACTION94.3059
2.302-2.4260.2861160.2142492X-RAY DIFFRACTION92.9106
2.426-2.5730.31180.2142299X-RAY DIFFRACTION90.8647
2.573-2.750.2811150.2212080X-RAY DIFFRACTION86.6561
2.75-2.970.327890.2311953X-RAY DIFFRACTION87.377
2.97-3.2520.2711100.2251710X-RAY DIFFRACTION84.9673
3.252-3.6340.235920.2231553X-RAY DIFFRACTION83.6724
3.634-4.1920.266700.2131395X-RAY DIFFRACTION84.4867
4.192-5.1250.213560.2021198X-RAY DIFFRACTION85.1324
5.125-7.2090.225460.2331056X-RAY DIFFRACTION94.9182
7.209-49.20.243340.193616X-RAY DIFFRACTION96.2963

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