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- PDB-7scm: Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2 -

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Basic information

Entry
Database: PDB / ID: 7scm
TitleCrystal Structure of Ancestral Amniote Cadherin-23 EC1-2
ComponentsCadherin 23
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / ADHESION / CALCIUM-BINDING PROTEIN / EVOLUTION
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.272 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
DepositionSep 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 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
B: Cadherin 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,36713
Polymers44,9802
Non-polymers38811
Water3,279182
1
A: Cadherin 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6726
Polymers22,4901
Non-polymers1825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cadherin 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6957
Polymers22,4901
Non-polymers2056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.109, 73.109, 381.934
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-439-

HOH

21A-510-

HOH

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Components

#1: Protein Cadherin 23


Mass: 22489.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIPL
#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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris pH 7.5 3 M Sodium formate Ancestral Amniote Protocadherin-15 EC1-2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 29083 / % possible obs: 100 % / Redundancy: 26.8 % / Rrim(I) all: 0.492 / Net I/σ(I): 16
Reflection shellResolution: 2.27→2.34 Å / Num. unique obs: 1389 / Rrim(I) all: 4.487 / % possible all: 99.9

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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: 2.272→44.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.19 / SU B: 5.886 / SU ML: 0.136 / Average fsc free: 0.9173 / Average fsc work: 0.9308 / Cross valid method: FREE R-VALUE / ESU R: 0.216 / ESU R Free: 0.193
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2379 1423 4.918 %
Rwork0.1901 27509 -
all0.192 --
obs-28932 98.909 %
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: 35.737 Å2
Baniso -1Baniso -2Baniso -3
1-1.556 Å20.778 Å20 Å2
2--1.556 Å2-0 Å2
3----5.049 Å2
Refinement stepCycle: LAST / Resolution: 2.272→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 11 182 3355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133238
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152987
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.6484432
X-RAY DIFFRACTIONr_angle_other_deg1.251.5746864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2945406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.25223.52179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37715487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6531518
X-RAY DIFFRACTIONr_chiral_restr0.0670.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02765
X-RAY DIFFRACTIONr_nbd_refined0.2470.2484
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.22655
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21543
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21664
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2124
X-RAY DIFFRACTIONr_metal_ion_refined0.160.248
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3310.23
X-RAY DIFFRACTIONr_nbd_other0.1590.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.215
X-RAY DIFFRACTIONr_mcbond_it2.753.4881624
X-RAY DIFFRACTIONr_mcbond_other2.7453.4861623
X-RAY DIFFRACTIONr_mcangle_it4.2265.222027
X-RAY DIFFRACTIONr_mcangle_other4.2255.2232028
X-RAY DIFFRACTIONr_scbond_it3.8474.0511614
X-RAY DIFFRACTIONr_scbond_other3.8214.0431612
X-RAY DIFFRACTIONr_scangle_it6.2875.862404
X-RAY DIFFRACTIONr_scangle_other6.2925.8592404
X-RAY DIFFRACTIONr_lrange_it8.35440.393325
X-RAY DIFFRACTIONr_lrange_other8.21740.2433297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.272-2.3310.309770.281696X-RAY DIFFRACTION85.4046
2.331-2.3950.356950.2651954X-RAY DIFFRACTION100
2.395-2.4640.3681050.2451883X-RAY DIFFRACTION100
2.464-2.540.313990.251850X-RAY DIFFRACTION100
2.54-2.6230.282820.2371799X-RAY DIFFRACTION100
2.623-2.7150.313820.2321740X-RAY DIFFRACTION100
2.715-2.8170.2631030.2241682X-RAY DIFFRACTION100
2.817-2.9320.253790.2111627X-RAY DIFFRACTION100
2.932-3.0620.231740.1991561X-RAY DIFFRACTION100
3.062-3.2110.241690.1931494X-RAY DIFFRACTION100
3.211-3.3850.228830.1881431X-RAY DIFFRACTION100
3.385-3.5890.211670.1751356X-RAY DIFFRACTION99.9298
3.589-3.8360.216610.1541308X-RAY DIFFRACTION99.927
3.836-4.1420.2600.161205X-RAY DIFFRACTION100
4.142-4.5360.178660.1391129X-RAY DIFFRACTION100
4.536-5.0680.174660.1391006X-RAY DIFFRACTION100
5.068-5.8460.216510.153920X-RAY DIFFRACTION100
5.846-7.1450.22440.165808X-RAY DIFFRACTION100
7.145-10.0410.175310.162648X-RAY DIFFRACTION100
10.041-44.930.271290.233412X-RAY DIFFRACTION98

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