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- PDB-7sgx: Crystal Structure of Turtle Cadherin-23 EC1-2 -

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Basic information

Entry
Database: PDB / ID: 7sgx
TitleCrystal Structure of Turtle Cadherin-23 EC1-2
ComponentsCadherin 23
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / ADHESION / CALCIUM-BINDING PROTEIN
Biological speciesChelonia mydas (Green sea turtle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 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
DepositionOct 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 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
C: Cadherin 23
D: Cadherin 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,31339
Polymers96,8154
Non-polymers1,49835
Water86548
1
A: Cadherin 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,61210
Polymers24,2041
Non-polymers4089
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cadherin 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5249
Polymers24,2041
Non-polymers3218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cadherin 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,56410
Polymers24,2041
Non-polymers3619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cadherin 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,61210
Polymers24,2041
Non-polymers4089
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.984, 94.984, 358.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Cadherin 23


Mass: 24203.768 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: This sequence matches record XP_007054748.1 at NCBI: https://www.ncbi.nlm.nih.gov/protein/XP_007054748.1/?report=fasta
Source: (gene. exp.) Chelonia mydas (Green sea turtle) / Production host: Escherichia coli (E. coli)
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 4.18 Å3/Da / Density % sol: 70.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.7 / Details: 0.1 M Tris pH 7.7 1.9 M CaCl2

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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: Nov 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.13→50 Å / Num. obs: 30114 / % possible obs: 99.8 % / Redundancy: 12.1 % / Rrim(I) all: 0.297 / Net I/σ(I): 12.559
Reflection shellResolution: 3.13→3.2 Å / Num. unique obs: 1456 / Rrim(I) all: 2.187 / % possible all: 100

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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: 3.13→49.056 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.87 / SU B: 24.974 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / ESU R: 1.34 / ESU R Free: 0.474
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3103 1525 5.091 %
Rwork0.2529 28430 -
all0.256 --
obs-29955 99.393 %
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: 99.691 Å2
Baniso -1Baniso -2Baniso -3
1-5.87 Å2-0 Å20 Å2
2--5.87 Å20 Å2
3----11.741 Å2
Refinement stepCycle: LAST / Resolution: 3.13→49.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6424 0 45 48 6517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136570
X-RAY DIFFRACTIONr_bond_other_d0.0030.0156057
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.6418971
X-RAY DIFFRACTIONr_angle_other_deg1.0621.57613903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0725822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29623.534365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26415996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6671536
X-RAY DIFFRACTIONr_chiral_restr0.0440.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021562
X-RAY DIFFRACTIONr_nbd_refined0.2020.21242
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.25691
X-RAY DIFFRACTIONr_nbtor_refined0.1560.23017
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0670.23442
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2153
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0510.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1760.257
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1360.211
X-RAY DIFFRACTIONr_nbd_other0.1610.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.23
X-RAY DIFFRACTIONr_mcbond_it5.13210.5083300
X-RAY DIFFRACTIONr_mcbond_other5.12910.5073299
X-RAY DIFFRACTIONr_mcangle_it8.3715.7474118
X-RAY DIFFRACTIONr_mcangle_other8.3715.7494119
X-RAY DIFFRACTIONr_scbond_it4.63110.9453270
X-RAY DIFFRACTIONr_scbond_other4.6310.9443271
X-RAY DIFFRACTIONr_scangle_it7.7916.2254853
X-RAY DIFFRACTIONr_scangle_other7.7916.2244854
X-RAY DIFFRACTIONr_lrange_it12.864121.5956754
X-RAY DIFFRACTIONr_lrange_other12.864121.596755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.13-3.2090.4351010.4181950X-RAY DIFFRACTION94.2122
3.209-3.2970.4311100.3892018X-RAY DIFFRACTION100
3.297-3.3920.4291150.3581958X-RAY DIFFRACTION99.9518
3.392-3.4970.464890.3381897X-RAY DIFFRACTION99.6488
3.497-3.6110.3941020.3111851X-RAY DIFFRACTION99.9488
3.611-3.7380.299880.271788X-RAY DIFFRACTION100
3.738-3.8790.2871010.2411722X-RAY DIFFRACTION100
3.879-4.0370.289920.2351667X-RAY DIFFRACTION100
4.037-4.2160.313910.211620X-RAY DIFFRACTION100
4.216-4.4210.265890.1971520X-RAY DIFFRACTION100
4.421-4.660.199860.1781466X-RAY DIFFRACTION99.6789
4.66-4.9420.275690.1771416X-RAY DIFFRACTION99.9327
4.942-5.2820.242680.1911334X-RAY DIFFRACTION99.8576
5.282-5.7030.289640.2161225X-RAY DIFFRACTION100
5.703-6.2450.304670.2141148X-RAY DIFFRACTION100
6.245-6.9780.35510.2391042X-RAY DIFFRACTION99.0036
6.978-8.050.313360.198956X-RAY DIFFRACTION100
8.05-9.840.207450.22811X-RAY DIFFRACTION100
9.84-13.8370.334370.279642X-RAY DIFFRACTION97.6978
13.837-49.0560.42240.404399X-RAY DIFFRACTION97.2414

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