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- PDB-6cg6: mouse cadherin-10 EC1-2 adhesive fragment -

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Basic information

Entry
Database: PDB / ID: 6cg6
Titlemouse cadherin-10 EC1-2 adhesive fragment
ComponentsCadherin-10
KeywordsCELL ADHESION / Cadherin EC domain Dimer Extracellular
Function / homology
Function and homology information


: / : / Adherens junctions interactions / multicellular organism development / cell-cell adhesion via plasma-membrane adhesion molecules / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / cell-cell junction assembly / adherens junction organization / homophilic cell adhesion via plasma membrane adhesion molecules ...: / : / Adherens junctions interactions / multicellular organism development / cell-cell adhesion via plasma-membrane adhesion molecules / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / cell-cell junction assembly / adherens junction organization / homophilic cell adhesion via plasma membrane adhesion molecules / GABA-ergic synapse / adherens junction / cell morphogenesis / cadherin binding / glutamatergic synapse / calcium ion binding
Similarity search - Function
Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. ...Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.707 Å
AuthorsBrasch, J. / Harrison, O.J. / Shapiro, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM062270 United States
National Science Foundation (NSF, United States)MCB- 0918535 United States
CitationJournal: Cell Rep / Year: 2018
Title: Homophilic and Heterophilic Interactions of Type II Cadherins Identify Specificity Groups Underlying Cell-Adhesive Behavior.
Authors: Brasch, J. / Katsamba, P.S. / Harrison, O.J. / Ahlsen, G. / Troyanovsky, R.B. / Indra, I. / Kaczynska, A. / Kaeser, B. / Troyanovsky, S. / Honig, B. / Shapiro, L.
History
DepositionFeb 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cadherin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4936
Polymers23,1481
Non-polymers3465
Water46826
1
A: Cadherin-10
hetero molecules

A: Cadherin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,98612
Polymers46,2952
Non-polymers69110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3160 Å2
ΔGint-42 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.524, 87.524, 67.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cadherin-10 / / T2-cadherin


Mass: 23147.639 Da / Num. of mol.: 1 / Fragment: EC1-2 (UNP residues 55-261)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh10 / Production host: Escherichia coli (E. coli) / References: UniProt: P70408
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6% v/v 2-propanol, 0.1 M MES, pH 6.0, 0.2 M calcium acetate, cryoprotectant: 30% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 18, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 7545 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.7
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 1.041 / Num. unique obs: 732

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CGU

6cgu


Resolution: 2.707→19.735 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.39
RfactorNum. reflection% reflection
Rfree0.2833 376 4.98 %
Rwork0.2377 --
obs0.2401 7545 99.87 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 2.707→19.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 18 26 1672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021679
X-RAY DIFFRACTIONf_angle_d0.5022277
X-RAY DIFFRACTIONf_dihedral_angle_d14.81005
X-RAY DIFFRACTIONf_chiral_restr0.046250
X-RAY DIFFRACTIONf_plane_restr0.003300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7067-3.09710.42341220.32342328X-RAY DIFFRACTION100
3.0971-3.89710.32611240.25752357X-RAY DIFFRACTION100
3.8971-19.73570.23361300.20772484X-RAY DIFFRACTION100

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