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- PDB-1zvn: Crystal structure of chick MN-cadherin EC1 -

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Basic information

Entry
Database: PDB / ID: 1zvn
TitleCrystal structure of chick MN-cadherin EC1
ComponentsCadherin 1
KeywordsCELL ADHESION / cadherin
Function / homology
Function and homology information


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 junction / cell morphogenesis / membrane => GO:0016020 ...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 junction / cell morphogenesis / membrane => GO:0016020 / cadherin binding / 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
Cadherin-20 / Cadherin-20
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å
AuthorsPatel, S.D. / Ciatto, C. / Chen, C.P. / Bahna, F. / Schieren, I. / Rajebhosale, M. / Jessell, T.M. / Honig, B. / Shapiro, L. / Price, S.R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Type II cadherin ectodomain structures: implications for classical cadherin specificity.
Authors: Patel, S.D. / Ciatto, C. / Chen, C.P. / Bahna, F. / Rajebhosale, M. / Arkus, N. / Schieren, I. / Jessell, T.M. / Honig, B. / Price, S.R. / Shapiro, L.
History
DepositionJun 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 10, 2013Group: Structure summary
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cadherin 1
B: Cadherin 1


Theoretical massNumber of molelcules
Total (without water)22,6752
Polymers22,6752
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-24 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.322, 76.155, 37.073
Angle α, β, γ (deg.)90.00, 96.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cadherin 1 / F-cadherin / MN-cadherin


Mass: 11337.545 Da / Num. of mol.: 2 / Fragment: UNP residues 60-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MNcadherin / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7ZYV7, UniProt: Q8QGH3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 60% saturated ammonium sulfate, 0.1M Bis-Tris pH 6.0, 7mM YbCl3 , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A11.065
SYNCHROTRONNSLS X9A20.9791
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 9, 2002
ADSC QUANTUM 42CCDSep 25, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1diamondSINGLE WAVELENGTHMx-ray1
2diamondSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0651
20.97911
ReflectionResolution: 2.16→20 Å / Num. all: 9670 / Num. obs: 9573 / % possible obs: 100 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.77
Reflection shellResolution: 2.16→2.24 Å / Rmerge(I) obs: 0.252 / Rsym value: 0.03 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.16→19.73 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.758 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.339 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 514 5.4 %RANDOM
Rwork0.16855 ---
all0.1686 9042 --
obs0.17264 9042 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.16→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 0 181 1739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211590
X-RAY DIFFRACTIONr_angle_refined_deg2.2531.952154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1175196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15724.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60215261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4221511
X-RAY DIFFRACTIONr_chiral_restr0.1050.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021235
X-RAY DIFFRACTIONr_nbd_refined0.2250.2640
X-RAY DIFFRACTIONr_nbtor_refined0.310.21062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2167
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.217
X-RAY DIFFRACTIONr_mcbond_it1.6741.5998
X-RAY DIFFRACTIONr_mcangle_it1.92421565
X-RAY DIFFRACTIONr_scbond_it3.0473674
X-RAY DIFFRACTIONr_scangle_it4.8014.5589
LS refinement shellResolution: 2.16→2.212 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 26 -
Rwork0.174 608 -
obs--91.35 %
Refinement TLS params.Method: refined / Origin x: 40.372 Å / Origin y: 23.104 Å / Origin z: 32.513 Å
111213212223313233
T-0.0415 Å2-0.0058 Å2-0.0034 Å2--0.0242 Å2-0.0094 Å2---0.0251 Å2
L0.4608 °20.3072 °2-0.1075 °2-0.7026 °20.0026 °2--0.8341 °2
S-0.0011 Å °-0.0329 Å °-0.0156 Å °0.0507 Å °-0.0063 Å °0.0139 Å °-0.0577 Å °0.0219 Å °0.0075 Å °

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