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- PDB-7n4p: Crystal Structure of Lizard Cadherin-23 EC1-2 -

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Basic information

Entry
Database: PDB / ID: 7n4p
TitleCrystal Structure of Lizard Cadherin-23 EC1-2
ComponentsCadherin 23
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / ADHESION / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


: / catenin complex / homophilic cell-cell adhesion / beta-catenin binding / neuron projection development / cell migration / cadherin binding / calcium ion binding
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 speciesAnolis carolinensis (green anole)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsNisler, C.R. / Sotomayor, M.
Funding support France, 1items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGP0056/2018 France
CitationJournal: Mol.Biol.Evol. / Year: 2023
Title: Interpreting the Evolutionary Echoes of a Protein Complex Essential for Inner-Ear Mechanosensation.
Authors: Nisler, C.R. / Narui, Y. / Scheib, E. / Choudhary, D. / Bowman, J.D. / Mandayam Bharathi, H. / Lynch, V.J. / Sotomayor, M.
History
DepositionJun 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.3Oct 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

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Assembly

Deposited unit
A: Cadherin 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,57710
Polymers24,2681
Non-polymers3099
Water2,666148
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)43.386, 43.386, 296.227
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-500-

HOH

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Components

#1: Protein Cadherin 23


Mass: 24267.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anolis carolinensis (green anole) / Gene: CDH23 / Plasmid: pET21a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIPL / References: UniProt: R4GAX0
#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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 1.1 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.097→50 Å / Num. obs: 17931 / % possible obs: 98.3 % / Redundancy: 6.5 % / Rrim(I) all: 0.106 / Net I/σ(I): 16.65
Reflection shellResolution: 2.097→2.14 Å / Num. unique obs: 736 / Rrim(I) all: 0.589 / % possible all: 86

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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: 2WHV

2whv


Resolution: 2.097→41.671 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.875 / SU ML: 0.159 / Cross valid method: FREE R-VALUE / ESU R: 0.196 / ESU R Free: 0.187
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2665 891 5.073 %
Rwork0.2108 16674 -
all0.214 --
obs-17565 98.475 %
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: 40.331 Å2
Baniso -1Baniso -2Baniso -3
1-1.921 Å2-0 Å2-0 Å2
2--1.921 Å2-0 Å2
3----3.843 Å2
Refinement stepCycle: LAST / Resolution: 2.097→41.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 9 148 1770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131675
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171543
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.6432294
X-RAY DIFFRACTIONr_angle_other_deg1.3961.5763546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9245212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34823.72394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05815258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.002159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02403
X-RAY DIFFRACTIONr_nbd_refined0.2270.2332
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.21520
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2826
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2124
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0910.22
X-RAY DIFFRACTIONr_metal_ion_refined0.2090.238
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.212
X-RAY DIFFRACTIONr_nbd_other0.1510.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2180.26
X-RAY DIFFRACTIONr_mcbond_it1.7732.6833
X-RAY DIFFRACTIONr_mcbond_other1.7742.596832
X-RAY DIFFRACTIONr_mcangle_it2.7973.8851041
X-RAY DIFFRACTIONr_mcangle_other2.7963.8891042
X-RAY DIFFRACTIONr_scbond_it2.0112.855842
X-RAY DIFFRACTIONr_scbond_other2.0082.847840
X-RAY DIFFRACTIONr_scangle_it3.2184.1771250
X-RAY DIFFRACTIONr_scangle_other3.2194.1761250
X-RAY DIFFRACTIONr_lrange_it6.6731.8871906
X-RAY DIFFRACTIONr_lrange_other6.25231.1711856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.097-2.1510.405460.3071060X-RAY DIFFRACTION86.2042
2.151-2.210.403500.281141X-RAY DIFFRACTION95.0519
2.21-2.2740.33520.2631149X-RAY DIFFRACTION98.9292
2.274-2.3440.375520.2411102X-RAY DIFFRACTION100
2.344-2.4210.338720.241100X-RAY DIFFRACTION100
2.421-2.5060.413650.2591013X-RAY DIFFRACTION100
2.506-2.60.191490.2361041X-RAY DIFFRACTION100
2.6-2.7060.347530.2371007X-RAY DIFFRACTION100
2.706-2.8270.305390.239934X-RAY DIFFRACTION100
2.827-2.9640.303460.235921X-RAY DIFFRACTION99.8967
2.964-3.1240.288520.204883X-RAY DIFFRACTION100
3.124-3.3140.211410.189816X-RAY DIFFRACTION100
3.314-3.5420.238550.201766X-RAY DIFFRACTION100
3.542-3.8250.279440.196740X-RAY DIFFRACTION100
3.825-4.1890.268400.165675X-RAY DIFFRACTION100
4.189-4.6810.166430.148621X-RAY DIFFRACTION99.5502
4.681-5.4020.214250.174583X-RAY DIFFRACTION99.6721
5.402-6.6070.235300.196472X-RAY DIFFRACTION99.6032
6.607-9.3070.199270.196392X-RAY DIFFRACTION99.0544
9.307-41.670.27100.256258X-RAY DIFFRACTION97.1014
Refinement TLS params.

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

IDL11 (°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)
12.1418-0.1159-0.69030.50231.48318.8269-0.04190.0532-0.32470.0435-0.04090.06130.6240.0230.08290.06280.0346-0.00560.1402-0.0230.10553.44.424-49.6238
20.88940.07471.26841.26251.76177.5736-0.02420.10740.05510.2112-0.11250.09830.2892-0.70420.13670.0422-0.04830.02650.2152-0.03270.05612.332315.9494-2.6669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 101
2X-RAY DIFFRACTION1ALLA302
3X-RAY DIFFRACTION1ALLA303 - 304
4X-RAY DIFFRACTION2ALLA102 - 206
5X-RAY DIFFRACTION2ALLA305 - 306
6X-RAY DIFFRACTION2ALLA301
7X-RAY DIFFRACTION2ALLA307

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