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- PDB-7t3s: Crystal Structure of Mouse Cadherin-23 EC8-9 -

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Basic information

Entry
Database: PDB / ID: 7t3s
TitleCrystal Structure of Mouse Cadherin-23 EC8-9
ComponentsCadherin-23
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / stereocilium ...cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / cell-cell adhesion via plasma-membrane adhesion molecules / photoreceptor ribbon synapse / stereocilium / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / photoreceptor cell maintenance / catenin complex / auditory receptor cell stereocilium organization / inner ear morphogenesis / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / locomotory behavior / sensory perception of sound / calcium ion transport / apical part of cell / cell adhesion / cadherin binding / centrosome / synapse / calcium ion binding / plasma membrane
Similarity search - Function
Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.966 Å
AuthorsSandhu, J.S. / De La Torre, P. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01 DC015271 United States
CitationJournal: to be published
Title: Crystal Structure of Mouse Cadherin-23 EC8-9
Authors: Sandhu, J.S. / De La Torre, P. / Sotomayor, M.
History
DepositionDec 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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
A: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6945
Polymers25,5511
Non-polymers1434
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.827, 56.194, 93.853
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cadherin-23 / Otocadherin


Mass: 25550.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q99PF4
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl 20% PEG 3350

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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: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.966→48.213 Å / Num. obs: 4947 / % possible obs: 98.9 % / Redundancy: 8.8 % / CC1/2: 0.966 / Net I/σ(I): 7.75
Reflection shellResolution: 2.97→3.02 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.77 / Num. unique obs: 224 / CC1/2: 0.809 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5tfl,5tfk

5tfl

5tfk


Resolution: 2.966→48.213 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.832 / SU B: 24.59 / SU ML: 0.446 / Cross valid method: FREE R-VALUE / ESU R Free: 0.538
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2992 253 5.201 %
Rwork0.2139 4611 -
all0.218 --
obs-4864 98.761 %
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: 52.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.865 Å20 Å2-0 Å2
2--6.044 Å20 Å2
3----2.179 Å2
Refinement stepCycle: LAST / Resolution: 2.966→48.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 4 1 1619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131644
X-RAY DIFFRACTIONr_bond_other_d0.0040.0141547
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.6542253
X-RAY DIFFRACTIONr_angle_other_deg1.071.5763570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9425208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.95323.08681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56615261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2541510
X-RAY DIFFRACTIONr_chiral_restr0.0420.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
X-RAY DIFFRACTIONr_nbd_refined0.1980.2267
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1410.21397
X-RAY DIFFRACTIONr_nbtor_refined0.1360.2759
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0630.2818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.229
X-RAY DIFFRACTIONr_metal_ion_refined0.1250.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1010.26
X-RAY DIFFRACTIONr_nbd_other0.1410.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.020.21
X-RAY DIFFRACTIONr_mcbond_it1.665.494838
X-RAY DIFFRACTIONr_mcbond_other1.6435.49837
X-RAY DIFFRACTIONr_mcangle_it2.9448.2261044
X-RAY DIFFRACTIONr_mcangle_other2.9458.2311045
X-RAY DIFFRACTIONr_scbond_it1.2765.685806
X-RAY DIFFRACTIONr_scbond_other1.2755.69807
X-RAY DIFFRACTIONr_scangle_it2.2718.4491209
X-RAY DIFFRACTIONr_scangle_other2.2718.4541210
X-RAY DIFFRACTIONr_lrange_it4.85862.671621
X-RAY DIFFRACTIONr_lrange_other4.85662.7111622
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
2.966-3.0430.191180.3423120.3333540.790.80893.22030.342
3.043-3.1260.503180.2713200.2813470.7190.83697.40630.271
3.126-3.2160.406200.293020.2973320.7310.84996.9880.29
3.216-3.3150.196130.2393050.2373260.9160.89597.5460.239
3.315-3.4230.351270.2362850.2473130.8710.90699.68050.236
3.423-3.5420.266150.222960.2223110.8780.9161000.22
3.542-3.6750.355190.2162680.2252870.8570.9151000.216
3.675-3.8240.324150.2282810.2322960.880.9141000.228
3.824-3.9930.341140.2012540.2072680.8610.9211000.201
3.993-4.1870.284110.2062680.212800.890.9299.64290.206
4.187-4.4110.346140.1832250.1952400.8970.92299.58330.183
4.411-4.6760.195110.1912440.1912560.9210.91999.60940.191
4.676-4.9960.26370.2112020.2122110.8860.91199.05210.211
4.996-5.3910.2390.2052120.2062210.8790.9251000.205
5.391-5.8990.356110.1821880.191990.8730.9391000.182
5.899-6.5830.70840.1891750.1961790.5190.9371000.189
6.583-7.5770.317120.191510.1991640.8770.95299.39020.19
7.577-9.2240.24980.1561400.1631480.9630.9631000.156
9.224-12.8120.15260.1741090.1731150.9730.9741000.174
12.812-48.2130.11110.236740.235780.95896.15380.236

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