PDB-7skh: Crystal Structure of Mouse Cadherin-23 EC16-17

ID or keywords:

Entry

Database: PDB / ID: 7skh

Title

Crystal Structure of Mouse Cadherin-23 EC16-17

Components

Cadherin-23

Keywords

CELL ADHESION / HEARING / MECHANOTRANSDUCTION / ADHESION / CALCIUM-BINDING PROTEIN

Function / homology

Function and homology information

kinocilium / equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / 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 ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.265 Å

Authors

Sudar, J.C. / Sandhu, J.S. / Sotomayor, M.

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal Structure of Mouse Cadherin-23 EC16-17
Authors: Sudar, J.C. / Sandhu, J.S. / Sotomayor, M.

History

Deposition	Oct 20, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 26, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7skh.cif.gz	178.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7skh.ent.gz	138.2 KB	Display	PDB format
PDBx/mmJSON format	7skh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sk/7skh ftp://data.pdbj.org/pub/pdb/validation_reports/sk/7skh	HTTPS FTP

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Related structure data

Related structure data	5wjmS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#99 - Mar 2008 Cadherin similarity (8)

Deposited unit

A: Cadherin-23

B: Cadherin-23

hetero molecules

50.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cadherin-23

hetero molecules

defined by author&software
Evidence: gel filtration
25.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cadherin-23

hetero molecules

defined by author&software
25.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.861, 90.861, 170.680
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Cadherin-23 / Otocadherin Mass: 25183.049 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET21a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 RIPL / References: UniProt: Q99PF4
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.5 Å³/Da / Density % sol: 65 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M MMT pH 9.0 25% PEG 1500

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 8, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97911 Å / Relative weight: 1
Reflection	Resolution: 2.265→50 Å / Num. obs: 34006 / % possible obs: 99 % / Redundancy: 22.3 % / CC_1/2: 0.993 / Net I/σ(I): 30.5
Reflection shell	Resolution: 2.265→2.31 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 3 / Num. unique obs: 1478 / CC_1/2: 0.777 / % possible all: 89.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5WJM

5wjm

Resolution: 2.265→48.267 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.923 / WR_factor R_free: 0.252 / WR_factor R_work: 0.209 / SU B: 10.962 / SU ML: 0.139 / Average fsc free: 0.9114 / Average fsc work: 0.9292 / Cross valid method: FREE R-VALUE / ESU R: 0.214 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2517	1654	4.996 %
R_work	0.2087	31451	-
all	0.211	-	-
obs	-	33105	97.242 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 60.786 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.531 Å²	0 Å²	0 Å²
2-	-	-1.531 Å²	0 Å²
3-	-	-	3.061 Å²

Refinement step

Cycle: LAST / Resolution: 2.265→48.267 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3270	0	6	104	3380

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	3416
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.014	3200
X-RAY DIFFRACTION	r_angle_refined_deg	1.585	1.651	4687
X-RAY DIFFRACTION	r_angle_other_deg	1.235	1.577	7352
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.912	5	432
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.614	21.809	199
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.16	15	530
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.577	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	471
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3914
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	788
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	527
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.175	0.2	2817
X-RAY DIFFRACTION	r_nbtor_refined	0.153	0.2	1554
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.072	0.2	1613
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	114
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.092	0.2	4
X-RAY DIFFRACTION	r_metal_ion_refined	0.086	0.2	26
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.172	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.188	0.2	56
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.277	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	1.456	3.232	1689
X-RAY DIFFRACTION	r_mcbond_other	1.455	3.23	1688
X-RAY DIFFRACTION	r_mcangle_it	2.209	4.835	2107
X-RAY DIFFRACTION	r_mcangle_other	2.208	4.838	2108
X-RAY DIFFRACTION	r_scbond_it	1.73	3.47	1727
X-RAY DIFFRACTION	r_scbond_other	1.729	3.472	1728
X-RAY DIFFRACTION	r_scangle_it	2.761	5.128	2571
X-RAY DIFFRACTION	r_scangle_other	2.76	5.131	2572
X-RAY DIFFRACTION	r_lrange_it	4.431	37.021	3426
X-RAY DIFFRACTION	r_lrange_other	4.4	36.925	3414

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.265-2.324	0.347	118	0.291	2006	X-RAY DIFFRACTION	86.2713
2.324-2.388	0.332	111	0.274	2187	X-RAY DIFFRACTION	95.2736
2.388-2.457	0.313	120	0.242	2169	X-RAY DIFFRACTION	98.2825
2.457-2.533	0.305	109	0.228	2129	X-RAY DIFFRACTION	98.5035
2.533-2.616	0.271	101	0.215	2072	X-RAY DIFFRACTION	98.1925
2.616-2.707	0.282	118	0.212	1981	X-RAY DIFFRACTION	98.3138
2.707-2.809	0.25	100	0.208	1952	X-RAY DIFFRACTION	99.2263
2.809-2.924	0.279	101	0.209	1900	X-RAY DIFFRACTION	99.5027
2.924-3.054	0.254	101	0.212	1810	X-RAY DIFFRACTION	99.687
3.054-3.203	0.235	104	0.221	1714	X-RAY DIFFRACTION	99.8901
3.203-3.376	0.302	82	0.24	1694	X-RAY DIFFRACTION	99.8875
3.376-3.58	0.296	81	0.241	1573	X-RAY DIFFRACTION	99.8792
3.58-3.827	0.243	63	0.207	1502	X-RAY DIFFRACTION	99.8724
3.827-4.132	0.244	68	0.183	1406	X-RAY DIFFRACTION	99.7969
4.132-4.526	0.185	52	0.166	1295	X-RAY DIFFRACTION	98.8261
4.526-5.058	0.165	56	0.158	1174	X-RAY DIFFRACTION	98.6367
5.058-5.836	0.212	52	0.176	1004	X-RAY DIFFRACTION	95.7389
5.836-7.138	0.286	50	0.226	830	X-RAY DIFFRACTION	91.1917
7.138-10.056	0.195	43	0.186	653	X-RAY DIFFRACTION	91.3386
10.056-48.267	0.307	24	0.272	400	X-RAY DIFFRACTION	89.8305

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.627	-1.6275	-0.3884	12.8782	4.685	4.4734	-0.2786	-0.7429	0.6362	1.3922	1.2426	-2.4497	0.1478	0.8667	-0.964	0.2105	0.1394	-0.2953	0.478	-0.4356	0.591	46.02	3.078	47.42
2	5.9166	2.2489	2.8549	1.9805	2.1663	4.1989	-0.0569	0.2799	0.0316	-0.1617	0.0388	0.065	-0.0264	-0.0206	0.0181	0.0383	-0.0052	0.0042	0.0276	-0.0061	0.026	18.455	-20.528	14.194
3	13.2882	-0.2593	7.0363	2.7993	-2.2146	6.6666	1.0375	-1.7766	-2.0706	0.5132	-0.032	-0.2487	0.646	-0.6631	-1.0055	0.4603	-0.1848	-0.4083	0.4018	0.4301	0.8653	70.088	-47.92	48.105
4	4.4035	-0.4013	2.5618	2.6998	-2.3907	5.2407	0.1781	0.1833	-0.5359	-0.2831	-0.0684	-0.2786	0.2454	0.1151	-0.1097	0.0367	0.0143	0.0132	0.0699	-0.0592	0.1399	41.099	-29.324	10.608

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1608 - 1714
2	X-RAY DIFFRACTION	1	ALL	A	1901 - 1902
3	X-RAY DIFFRACTION	2	ALL	A	1715 - 1822
4	X-RAY DIFFRACTION	2	ALL	A	1903
5	X-RAY DIFFRACTION	3	ALL	B	1607 - 1714
6	X-RAY DIFFRACTION	3	ALL	B	1902 - 1903
7	X-RAY DIFFRACTION	4	ALL	B	1715 - 1832
8	X-RAY DIFFRACTION	4	ALL	B	1901

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