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- PDB-3k6i: Crystal structure of chicken T-cadherin EC1 -

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Basic information

Entry
Database: PDB / ID: 3k6i
TitleCrystal structure of chicken T-cadherin EC1
ComponentsT-cadherin
KeywordsCELL ADHESION / T-cadherin / Alternative splicing / Calcium / 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: 1.13 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 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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: T-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9273
Polymers10,7961
Non-polymers1312
Water6,395355
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.153, 44.930, 56.666
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 10796.244 Da / Num. of mol.: 1 / Fragment: EC1 domain: UNP residues 140-237
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM Zn acetate, 20 % PEG 3350, pH 7.0, 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
DetectorType: ADSC QUANTUM 315 / Detector: CCD
Details: Horizontal focusing sagitally bent second mono crystal
RadiationMonochromator: Cryogenically cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 42837 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.7
Reflection shellResolution: 1.1→1.15 Å / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 6.4 / % possible all: 97.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3K6F

3k6f


Resolution: 1.13→18.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 1 / SU B: 0.819 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.158 2176 5.1 %RANDOM
Rwork0.142 ---
obs0.143 42834 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.37 Å2 / Biso mean: 13.631 Å2 / Biso min: 3.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--0.1 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.13→18.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 2 355 1117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022771
X-RAY DIFFRACTIONr_angle_refined_deg2.0412.0091045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.012598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45923.93933
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59315138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.509158
X-RAY DIFFRACTIONr_chiral_restr0.1030.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02581
X-RAY DIFFRACTIONr_nbd_refined0.2630.2379
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2532
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2285
X-RAY DIFFRACTIONr_metal_ion_refined0.0540.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.241
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0430.23
X-RAY DIFFRACTIONr_mcbond_it1.6591.5509
X-RAY DIFFRACTIONr_mcangle_it2.2712809
X-RAY DIFFRACTIONr_scbond_it2.8063283
X-RAY DIFFRACTIONr_scangle_it4.1014.5236
X-RAY DIFFRACTIONr_rigid_bond_restr1.5523792
X-RAY DIFFRACTIONr_sphericity_free4.5943357
X-RAY DIFFRACTIONr_sphericity_bonded3.8623760
LS refinement shellResolution: 1.13→1.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.139 162 -
Rwork0.129 2896 -
all-3058 -
obs--98.9 %

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