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- PDB-3k6d: Crystal structure of Xenopus laevis T-cadherin EC1 -

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Basic information

Entry
Database: PDB / ID: 3k6d
TitleCrystal structure of Xenopus laevis T-cadherin EC1
ComponentsT-cadherin
KeywordsCELL ADHESION / T-cadherin
Function / homology
Function and homology information


adenosinetriphosphatase / homophilic cell adhesion via plasma membrane adhesion molecules / calcium ion binding / plasma membrane
Similarity search - Function
Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cadherin 13 L homeolog precursor
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_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

Downloads & links

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Assembly

Deposited unit
A: T-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8632
Polymers10,7971
Non-polymers651
Water1,838102
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.910, 78.910, 62.577
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-201-

ZN

21A-101-

HOH

31A-106-

HOH

41A-116-

HOH

51A-138-

HOH

61A-142-

HOH

71A-173-

HOH

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Components

#1: Protein T-cadherin / LOC495024 protein


Mass: 10797.280 Da / Num. of mol.: 1 / Fragment: EC1 domain: UNP residues 136-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: cdh13, LOC495024 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5XHE3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
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: 1.8→30 Å / Num. obs: 17500 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 24.52 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→27.902 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.787 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.285 1736 9.93 %
Rwork0.227 --
obs0.227 17486 99.88 %
Solvent computationBsol: 68.29 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 66.01 Å2 / Biso mean: 31.143 Å2 / Biso min: 3.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-0 Å2
2--0.86 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 1 102 863
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d1.9161
X-RAY DIFFRACTIONf_bond_d0.0171
X-RAY DIFFRACTIONf_chiral_restr0.1141
X-RAY DIFFRACTIONf_dihedral_angle_d18.2931
X-RAY DIFFRACTIONf_plane_restr0.0081
X-RAY DIFFRACTIONf_nbd_refined4.1121
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
1.8-1.8190.273494X-RAY DIFFRACTION3290
1.819-1.8390.262499X-RAY DIFFRACTION3290
1.839-1.860.239473X-RAY DIFFRACTION3290
1.86-1.8820.236512X-RAY DIFFRACTION3290
1.882-1.9050.246474X-RAY DIFFRACTION3291
1.905-1.9290.249498X-RAY DIFFRACTION3290
1.929-1.9540.227492X-RAY DIFFRACTION3290
1.954-1.9810.213503X-RAY DIFFRACTION3290
1.981-2.010.252482X-RAY DIFFRACTION3290
2.01-2.0390.243485X-RAY DIFFRACTION3290
2.039-2.0710.232496X-RAY DIFFRACTION3290
2.071-2.1050.236497X-RAY DIFFRACTION3290
2.105-2.1420.247511X-RAY DIFFRACTION3290
2.142-2.1810.207473X-RAY DIFFRACTION3290
2.181-2.2220.23488X-RAY DIFFRACTION3291
2.222-2.2680.227500X-RAY DIFFRACTION3290
2.268-2.3170.231483X-RAY DIFFRACTION3290
2.317-2.3710.226502X-RAY DIFFRACTION3291
2.371-2.430.216495X-RAY DIFFRACTION3291
2.43-2.4960.246484X-RAY DIFFRACTION3290
2.496-2.5690.228492X-RAY DIFFRACTION3290
2.569-2.6520.238504X-RAY DIFFRACTION3290
2.652-2.7470.237493X-RAY DIFFRACTION3291
2.747-2.8570.23495X-RAY DIFFRACTION3290
2.857-2.9870.273485X-RAY DIFFRACTION3290
2.987-3.1440.223502X-RAY DIFFRACTION3290
3.144-3.3410.218486X-RAY DIFFRACTION3291
3.341-3.5980.202497X-RAY DIFFRACTION3289
3.598-3.9590.203484X-RAY DIFFRACTION3290
3.959-4.530.173488X-RAY DIFFRACTION3289
4.53-5.6990.2497X-RAY DIFFRACTION3290
5.699-27.9020.238486X-RAY DIFFRACTION3288

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