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- PDB-3k5s: Crystal structure of chicken T-cadherin EC1 EC2 -

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Basic information

Entry
Database: PDB / ID: 3k5s
TitleCrystal structure of chicken T-cadherin EC1 EC2
ComponentsCadherin-13
KeywordsSTRUCTURAL PROTEIN / Cadherin / calcium / cell adhesion / Alternative splicing / Cell membrane / Cleavage on pair of basic residues / Glycoprotein / GPI-anchor / Lipoprotein / Membrane
Function / homology
Function and homology information


Adherens junctions interactions / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / supramolecular fiber / catenin complex / cell-cell junction assembly / adherens junction organization / sprouting angiogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / side of membrane ...Adherens junctions interactions / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / supramolecular fiber / catenin complex / cell-cell junction assembly / adherens junction organization / sprouting angiogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / side of membrane / adherens junction / cell morphogenesis / cadherin binding / calcium ion binding / cell surface
Similarity search - Function
Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsShapiro, L. / Ciatto, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: T-cadherin structures reveal a novel adhesive binding mechanism
Authors: Ciatto, C. / Bahna, F. / Zampieri, N. / Vansteenhouse, H.C. / Katsamba, P.S. / Ahlsen, G. / Harrison, O.J. / Brasch, J. / Jin, X. / Posy, S. / Vendome, J. / Ranscht, B. / Jessell, T.M. / Honig, B. / Shapiro, L.
History
DepositionOct 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cadherin-13
B: Cadherin-13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7428
Polymers47,5022
Non-polymers2406
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-37 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.804, 79.188, 105.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cadherin-13 / / Truncated cadherin / T-cadherin / T-cad


Mass: 23750.883 Da / Num. of mol.: 2 / Fragment: Domains EC1 and EC2 (UNP residues 140 to 355)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CDH13 / Production host: Escherichia coli (E. coli) / References: UniProt: P33150
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% MPD, 15% PEG 400, 50mM Na acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 10854 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.121
Reflection shellHighest resolution: 2.9 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameClassification
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29 Å /
RfactorNum. reflection
Rfree0.294 -
Rwork0.213 -
obs-10854
Refinement stepCycle: LAST / Resolution: 2.9→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 6 27 3363

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