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- PDB-4zmo: Crystal structure of human P-cadherin (ss-dimer K14E) -

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Basic information

Entry
Database: PDB / ID: 4zmo
TitleCrystal structure of human P-cadherin (ss-dimer K14E)
ComponentsCadherin-3
KeywordsCELL ADHESION / classical cadherin P-cadherin cell-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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3713
Polymers23,2911
Non-polymers802
Water55831
1
A: Cadherin-3
hetero molecules

A: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7426
Polymers46,5812
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1600 Å2
ΔGint-10 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.380, 81.230, 48.990
Angle α, β, γ (deg.)90.00, 105.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23290.748 Da / Num. of mol.: 1 / Mutation: K14E
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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 4.87 Å3/Da / Density % sol: 74.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 26% PEG 4,000 170 lithium sulfate 15% glycerol 85 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: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→42.43 Å / Num. obs: 15628 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.8
Reflection shellResolution: 2.48→2.61 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.5 / % possible all: 91.3

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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: 2.48→42.43 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.914 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23549 760 4.9 %RANDOM
Rwork0.19863 ---
obs0.20046 14868 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.379 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20.2 Å2
2--1.79 Å20 Å2
3----2.22 Å2
Refinement stepCycle: 1 / Resolution: 2.48→42.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 2 31 1672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191674
X-RAY DIFFRACTIONr_bond_other_d0.0010.021545
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9532279
X-RAY DIFFRACTIONr_angle_other_deg0.79833585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2745212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3525.78976
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74715271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.808156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211889
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02343
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_it2.2623.482851
X-RAY DIFFRACTIONr_mcbond_other2.2633.48850
X-RAY DIFFRACTIONr_mcangle_it3.3945.2221062
X-RAY DIFFRACTIONr_mcangle_other3.3935.2241063
X-RAY DIFFRACTIONr_scbond_it2.9613.818823
X-RAY DIFFRACTIONr_scbond_other2.9613.812820
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6115.5861216
X-RAY DIFFRACTIONr_long_range_B_refined6.02627.7631736
X-RAY DIFFRACTIONr_long_range_B_other6.01527.6961727
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.48→2.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 40 -
Rwork0.309 979 -
obs--86.58 %
Refinement TLS params.Method: refined / Origin x: -18.028 Å / Origin y: 29.6679 Å / Origin z: 16.1645 Å
111213212223313233
T0.0713 Å2-0.074 Å20.0127 Å2-0.1096 Å2-0.0403 Å2--0.0604 Å2
L4.5832 °22.3833 °2-1.1053 °2-1.5706 °2-0.6465 °2--1.2382 °2
S0.1353 Å °-0.2 Å °-0.2394 Å °0.0606 Å °-0.1883 Å °-0.0565 Å °0.1989 Å °-0.1466 Å °0.053 Å °

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