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- PDB-4zmw: Crystal structure of human P-cadherin (enc-X-dimer) -

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Basic information

Entry
Database: PDB / ID: 4zmw
TitleCrystal structure of human P-cadherin (enc-X-dimer)
ComponentsCadherin-3
KeywordsCELL ADHESION / dimerization / conformational change
Function / homology
Function and homology information


: / negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / calcium-dependent cell-cell adhesion / cell-cell adhesion mediated by cadherin / adherens junction organization / catenin complex ...: / negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / calcium-dependent cell-cell adhesion / cell-cell adhesion mediated by cadherin / adherens junction organization / catenin complex / cell-cell junction assembly / retina homeostasis / Adherens junctions interactions / positive regulation of insulin-like growth factor receptor signaling pathway / keratinization / homophilic cell-cell adhesion / visual perception / adherens junction / negative regulation of transforming growth factor beta receptor signaling pathway / beta-catenin binding / cell morphogenesis / cell junction / positive regulation of canonical Wnt signaling pathway / cell migration / cell adhesion / cadherin binding / calcium ion binding / positive regulation of gene expression / plasma membrane / cytoplasm
Similarity search - Function
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 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
NICKEL (II) ION / Cadherin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCaaveiro, J.M.M. / Kudo, S. / Tsumoto, K.
CitationJournal: Structure / Year: 2016
Title: Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism
Authors: Kudo, S. / Caaveiro, J.M. / Tsumoto, K.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cadherin-3
B: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,76415
Polymers46,8142
Non-polymers95013
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-141 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.369, 106.810, 77.579
Angle α, β, γ (deg.)90.00, 94.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23407.039 Da / Num. of mol.: 2 / Fragment: UNP residues 108-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH3, CDHP / Plasmid: Champion pET SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22223
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: 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

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Sample preparation

CrystalDensity Matthews: 4.16 Å3/Da / Density % sol: 70.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.15 M Lithium sulfate 7.5 mM nickel sulfate 100 mM TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.02 Å / Num. obs: 33629 / % possible obs: 98.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 4.8 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZMN

4zmn


Resolution: 2.3→47.02 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.862 / SU B: 6.571 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27558 1798 5.3 %RANDOM
Rwork0.23036 ---
obs0.23277 31831 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.492 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20.29 Å2
2---2.43 Å20 Å2
3---3.05 Å2
Refinement stepCycle: 1 / Resolution: 2.3→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 41 102 3417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193390
X-RAY DIFFRACTIONr_bond_other_d0.0010.023125
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9614622
X-RAY DIFFRACTIONr_angle_other_deg0.80437252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0075430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32625.762151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76615549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3841512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213789
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02691
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5693.5571708
X-RAY DIFFRACTIONr_mcbond_other2.5683.5561707
X-RAY DIFFRACTIONr_mcangle_it4.0625.3222133
X-RAY DIFFRACTIONr_mcangle_other4.0615.3232134
X-RAY DIFFRACTIONr_scbond_it3.2783.971682
X-RAY DIFFRACTIONr_scbond_other2.8053.9331652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4715.752444
X-RAY DIFFRACTIONr_long_range_B_refined6.79927.8943554
X-RAY DIFFRACTIONr_long_range_B_other6.727.9123522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 98 -
Rwork0.266 2111 -
obs--88.11 %

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