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- PDB-8tri: Crystal Structure of Mouse Cadherin-23 EC25-MAD28 F2894A -

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Basic information

Entry
Database: PDB / ID: 8tri
TitleCrystal Structure of Mouse Cadherin-23 EC25-MAD28 F2894A
ComponentsCadherin-23
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / ADHESION / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / kinocilium / inner ear auditory receptor cell differentiation / calcium-dependent cell-cell adhesion / stereocilium ...equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / kinocilium / inner ear auditory receptor cell differentiation / calcium-dependent cell-cell adhesion / stereocilium / photoreceptor cell maintenance / auditory receptor cell stereocilium organization / inner ear morphogenesis / homophilic cell-cell adhesion / inner ear development / cochlea development / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / locomotory behavior / sensory perception of sound / calcium ion transport / cell adhesion / calcium ion binding / synapse / centrosome / plasma membrane
Similarity search - Function
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: 3.716 Å
AuthorsAshraf, Q. / 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 EC25-MAD28 F2894A
Authors: Ashraf, Q. / Sotomayor, M.
History
DepositionAug 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 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: Cadherin-23
B: Cadherin-23
C: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,43421
Polymers159,7133
Non-polymers72118
Water1629
1
A: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4787
Polymers53,2381
Non-polymers2406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4787
Polymers53,2381
Non-polymers2406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4787
Polymers53,2381
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.994, 164.657, 183.634
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


Mass: 53237.551 Da / Num. of mol.: 3 / Fragment: residues 2603-3065 / Mutation: F2894A
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.: 18 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 6.96 Å3/Da / Density % sol: 82.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 1.25 M Lithium Acetate, 0.1 M MES pH 7.2, 25% glycerol (cryo)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 47174 / % possible obs: 99.9 % / Redundancy: 10.4 % / CC1/2: 0.981 / CC star: 0.995 / Net I/σ(I): 11.5
Reflection shellResolution: 3.7→3.76 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 2309 / CC1/2: 0.56 / CC star: 0.847 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.716→49.563 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.187 / SU B: 22.316 / SU ML: 0.306 / Average fsc free: 0.9625 / Average fsc work: 0.9768 / Cross valid method: FREE R-VALUE / ESU R: 1.416 / ESU R Free: 0.422
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2294 2329 4.951 %
Rwork0.1871 44714 -
all0.189 --
obs-47043 98.678 %
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: 124.855 Å2
Baniso -1Baniso -2Baniso -3
1-4.035 Å20 Å20 Å2
2--2.426 Å2-0 Å2
3----6.461 Å2
Refinement stepCycle: LAST / Resolution: 3.716→49.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10490 0 18 9 10517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01210687
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610158
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.65314566
X-RAY DIFFRACTIONr_angle_other_deg0.4991.57123283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.42851320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.794588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.336101751
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.87110552
X-RAY DIFFRACTIONr_chiral_restr0.0610.21681
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212850
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022482
X-RAY DIFFRACTIONr_nbd_refined0.2750.22424
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2380.210536
X-RAY DIFFRACTIONr_nbtor_refined0.1980.25176
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.26383
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2344
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0810.27
X-RAY DIFFRACTIONr_metal_ion_refined0.2660.264
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4220.226
X-RAY DIFFRACTIONr_nbd_other0.360.2127
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1060.22
X-RAY DIFFRACTIONr_mcbond_it23.17911.9085298
X-RAY DIFFRACTIONr_mcbond_other23.16611.9095298
X-RAY DIFFRACTIONr_mcangle_it31.45621.4586612
X-RAY DIFFRACTIONr_mcangle_other31.45421.4596613
X-RAY DIFFRACTIONr_scbond_it27.75912.775389
X-RAY DIFFRACTIONr_scbond_other27.75712.775390
X-RAY DIFFRACTIONr_scangle_it36.62423.0717954
X-RAY DIFFRACTIONr_scangle_other36.62223.0717955
X-RAY DIFFRACTIONr_lrange_it40.939153.87444518
X-RAY DIFFRACTIONr_lrange_other40.939153.87344519
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
3.716-3.8120.321330.29627590.29734680.9350.94783.3910.296
3.812-3.9150.341700.27632220.2834020.9330.95299.70610.276
3.915-4.0280.3081560.24830870.25132530.9360.96299.69260.248
4.028-4.1510.2771560.21930230.22231810.9480.9799.93710.219
4.151-4.2870.2741560.20529500.20831060.9480.9741000.205
4.287-4.4360.2511650.18828350.19130000.9580.9771000.188
4.436-4.6020.2531270.1727880.17329150.9590.9821000.17
4.602-4.7880.231140.15226620.15527760.9680.9861000.152
4.788-4.9990.1811430.13725390.1426820.980.9891000.137
4.999-5.240.1741330.13624540.13825870.9850.991000.136
5.24-5.520.221360.16323030.16724390.9760.9871000.163
5.52-5.850.2531100.17922210.18323310.9680.9851000.179
5.85-6.2480.2451090.1820720.18321830.9710.98599.90840.18
6.248-6.740.2181060.17719600.17920660.9780.9841000.177
6.74-7.370.218980.16218150.16519130.9790.9851000.162
7.37-8.2170.215900.14616430.14917350.9730.98799.88470.146
8.217-9.4450.176680.16414550.16515230.9850.9861000.164
9.445-11.4640.166660.1712720.1713380.9860.9861000.17
11.464-15.7950.19590.19110050.19110650.9820.98299.90610.191
15.795-49.5630.214340.2496490.2476830.9830.9741000.249

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