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- PDB-1ncj: N-CADHERIN, TWO-DOMAIN FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1ncj
TitleN-CADHERIN, TWO-DOMAIN FRAGMENT
ComponentsPROTEIN (N-CADHERIN)
KeywordsCELL ADHESION PROTEIN
Function / homology
Function and homology information


mesenchymal cell migration / regulation of oligodendrocyte progenitor proliferation / radial glial cell differentiation / neuroligin clustering involved in postsynaptic membrane assembly / regulation of postsynaptic density protein 95 clustering / positive regulation of synaptic vesicle clustering / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Adherens junctions interactions / gamma-catenin binding ...mesenchymal cell migration / regulation of oligodendrocyte progenitor proliferation / radial glial cell differentiation / neuroligin clustering involved in postsynaptic membrane assembly / regulation of postsynaptic density protein 95 clustering / positive regulation of synaptic vesicle clustering / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Adherens junctions interactions / gamma-catenin binding / synaptic vesicle clustering / desmosome / neuroepithelial cell differentiation / neural crest cell development / type B pancreatic cell development / fascia adherens / telencephalon development / neuronal stem cell population maintenance / alpha-catenin binding / calcium-dependent cell-cell adhesion / apicolateral plasma membrane / Myogenesis / glial cell differentiation / cell-cell adhesion mediated by cadherin / catenin complex / brain morphogenesis / cell-cell junction assembly / blood vessel morphogenesis / heterophilic cell-cell adhesion / cortical actin cytoskeleton / homophilic cell-cell adhesion / homeostasis of number of cells / intercalated disc / plasma membrane raft / striated muscle cell differentiation / protein localization to plasma membrane / adherens junction / negative regulation of canonical Wnt signaling pathway / cell-cell adhesion / sarcolemma / beta-catenin binding / cerebral cortex development / cell-cell junction / cell migration / presynapse / lamellipodium / protein phosphatase binding / basolateral plasma membrane / cell adhesion / positive regulation of MAPK cascade / apical plasma membrane / calcium ion binding / synapse / protein kinase binding / enzyme binding / cell surface / RNA binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherins / Cadherin conserved site / Cadherin domain signature. ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherins / 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
URANYL (VI) ION / Cadherin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsTamura, K. / Shan, W.-S. / Hendrickson, W.A. / Colman, D.R. / Shapiro, L.
CitationJournal: Neuron / Year: 1998
Title: Structure-function analysis of cell adhesion by neural (N-) cadherin.
Authors: Tamura, K. / Shan, W.S. / Hendrickson, W.A. / Colman, D.R. / Shapiro, L.
History
DepositionFeb 2, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (N-CADHERIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9945
Polymers23,6031
Non-polymers3904
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.000, 99.000, 136.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-401-

IUM

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Components

#1: Protein PROTEIN (N-CADHERIN)


Mass: 23603.465 Da / Num. of mol.: 1 / Fragment: TWO-DOMAIN FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Tissue: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: P15116
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2U

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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: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growpH: 5
Details: REMARK 280 CRYSTALLIZATION CONDITIONS: REMARK 280 HANGING DROP, 20MG/ML PROTEIN REMARK 280 50 MM NA ACETATE, PH 5.0, 15MM CACL2, REMARK 280 1MM UO2 ACETATE
Crystal grow
*PLUS
Method: vapor diffusion
Details: drop contains equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMNa acetate1reservoir
315 mM1reservoirCaCl2
41 mMuranyl acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. obs: 9451 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.93 / Rsym value: 0.93 / Net I/σ(I): 12.96
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.12 / Rsym value: 0.322 / % possible all: 97.7
Reflection shell
*PLUS
% possible obs: 97.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NCG AND 1EDH

1ncg

1edh


Resolution: 3.4→6 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.321 -5 %RANDOM
Rwork0.212 ---
obs-4581 97.4 %-
Displacement parametersBiso mean: 29.2 Å2
Refinement stepCycle: LAST / Resolution: 3.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 4 0 1855
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.9
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.4→3.55 Å / Total num. of bins used: 8 / % reflection obs: 97 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.9

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