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- PDB-4nqq: Crystal structure of mouse P-cadherin extracellular domains EC1-EC2 -

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Basic information

Entry
Database: PDB / ID: 4nqq
TitleCrystal structure of mouse P-cadherin extracellular domains EC1-EC2
ComponentsCadherin-3
KeywordsCELL ADHESION / Extracellular cadherin (EC) domain / Cell-Cell adhesion
Function / homology
Function and homology information


negative regulation of transforming growth factor beta2 production / : / negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / Adherens junctions interactions / positive regulation of melanin biosynthetic process / response to xenobiotic stimulus => GO:0009410 ...negative regulation of transforming growth factor beta2 production / : / negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / Adherens junctions interactions / positive regulation of melanin biosynthetic process / response to xenobiotic stimulus => GO:0009410 / cell-cell adhesion via plasma-membrane adhesion molecules / catenin complex / retina homeostasis / positive regulation of insulin-like growth factor receptor signaling pathway / keratinization / homophilic cell adhesion via plasma membrane adhesion molecules / adherens junction / wound healing / cell-cell adhesion / positive regulation of canonical Wnt signaling pathway / cell junction / membrane => GO:0016020 / cadherin binding / calcium ion binding / positive regulation of gene expression / plasma membrane / cytoplasm
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
COPPER (II) ION / Cadherin-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBrasch, J. / Shapiro, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural and energetic determinants of adhesive binding specificity in type I cadherins.
Authors: Vendome, J. / Felsovalyi, K. / Song, H. / Yang, Z. / Jin, X. / Brasch, J. / Harrison, O.J. / Ahlsen, G. / Bahna, F. / Kaczynska, A. / Katsamba, P.S. / Edmond, D. / Hubbell, W.L. / Shapiro, L. / Honig, B.
History
DepositionNov 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Cadherin-3
B: Cadherin-3
C: Cadherin-3
D: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,05827
Polymers93,9254
Non-polymers1,13323
Water1,36976
1
A: Cadherin-3
B: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,49713
Polymers46,9622
Non-polymers53511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-70 kcal/mol
Surface area23370 Å2
MethodPISA
2
C: Cadherin-3
D: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,56114
Polymers46,9622
Non-polymers59812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.085, 188.700, 53.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Cadherin-3 / Placental cadherin / P-cadherin


Mass: 23481.229 Da / Num. of mol.: 4
Fragment: extracellular domains EC1-EC2, UNP residues 100-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh3, Cdhp / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: P10287
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 38% PEG 6000, Bis-Tris pH 6.5, 0.35M Calcium chloride, 0.01M Copper (II) chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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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: Nov 2, 2012
RadiationMonochromator: Bent single Si(111) crystal (horizontal focusing and deflection)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. all: 21058 / Num. obs: 20958 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Redundancy: 6.3 %
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.6 / % possible all: 97.3

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Processing

Software
NameVersionClassification
MAR345data collection softwaredata collection
PHASERphasing
PHENIX(phenix.refine: dev_1186)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QVI

2qvi


Resolution: 3.2→20 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.269 1048 5 %
Rwork0.228 --
obs0.23 20958 99.2 %
all-21058 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6547 0 23 76 6646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016744
X-RAY DIFFRACTIONf_angle_d0.8969230
X-RAY DIFFRACTIONf_dihedral_angle_d10.2062502
X-RAY DIFFRACTIONf_chiral_restr0.0421025
X-RAY DIFFRACTIONf_plane_restr0.0041201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.3680.38051410.27892692X-RAY DIFFRACTION95
3.368-3.57790.3061470.26032788X-RAY DIFFRACTION99
3.5779-3.85230.28351490.23192831X-RAY DIFFRACTION100
3.8523-4.23670.2811490.21092827X-RAY DIFFRACTION100
4.2367-4.84210.24731510.19092874X-RAY DIFFRACTION100
4.8421-6.07210.26491510.23312877X-RAY DIFFRACTION100
6.0721-19.9990.23691600.23273021X-RAY DIFFRACTION100

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