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- PDB-5a2f: Two membrane distal IgSF domains of CD166 -

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Basic information

Entry
Database: PDB / ID: 5a2f
TitleTwo membrane distal IgSF domains of CD166
ComponentsCD166 ANTIGEN
KeywordsCELL ADHESION / ALCAM / ACTIVATED LEUKOCYTE CELL ADHESION PROTEIN / HUMAN
Function / homology
Function and homology information


: / L1CAM interactions / axon extension involved in axon guidance / motor neuron axon guidance / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / neuron projection extension / retinal ganglion cell axon guidance / plasma membrane => GO:0005886 / immunological synapse / adaptive immune response ...: / L1CAM interactions / axon extension involved in axon guidance / motor neuron axon guidance / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / neuron projection extension / retinal ganglion cell axon guidance / plasma membrane => GO:0005886 / immunological synapse / adaptive immune response / cell adhesion / external side of plasma membrane / axon / focal adhesion / signaling receptor binding / neuronal cell body / dendrite / signal transduction / extracellular exosome / identical protein binding
Similarity search - Function
CD166 antigen / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...CD166 antigen / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsChappell, P.E. / Johnson, S. / Lea, S.M. / Brown, M.H.
CitationJournal: Structure / Year: 2015
Title: Structures of Cd6 and its Ligand Cd166 Give Insight Into Their Interaction.
Authors: Chappell, P.E. / Garner, L.I. / Yan, J. / Metcalfe, C. / Hatherley, D. / Johnson, S. / Robinson, C.V. / Lea, S.M. / Brown, M.H.
History
DepositionMay 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD166 ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,61119
Polymers65,1751
Non-polymers1,43618
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.320, 72.320, 105.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CD166 ANTIGEN / ACTIVATED LEUKOCYTE CELL ADHESION MOLECULE / HUMAN CD166


Mass: 65175.082 Da / Num. of mol.: 1 / Fragment: TWO MEMBRANE DISTAL IGSF DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: CHO LEC 3.2.8.1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: Q13740
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.75 Å3/Da / Density % sol: 55.32 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M SODIUM HEPES, PH 7.5, 25% PEG-2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Aug 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.86→51.14 Å / Num. obs: 24110 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 13 % / Biso Wilson estimate: 27.37 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.1
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSVIA XIA2data reduction
AimlessVIA XIA2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CJJ

3cjj


Resolution: 1.86→21.09 Å / Cor.coef. Fo:Fc: 0.9319 / Cor.coef. Fo:Fc free: 0.9216 / SU R Cruickshank DPI: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.153 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.129
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 1229 5.11 %RANDOM
Rwork0.2217 ---
obs0.2225 24029 99.88 %-
Displacement parametersBiso mean: 34.12 Å2
Baniso -1Baniso -2Baniso -3
1-2.6248 Å20 Å20 Å2
2--2.6248 Å20 Å2
3----5.2496 Å2
Refine analyzeLuzzati coordinate error obs: 0.255 Å
Refinement stepCycle: LAST / Resolution: 1.86→21.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 92 186 2035
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0063745HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.936743HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d847SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes494HARMONIC5
X-RAY DIFFRACTIONt_it3745HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion13.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion253SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3719SEMIHARMONIC4
LS refinement shellResolution: 1.86→1.94 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2724 151 5.3 %
Rwork0.2482 2697 -
all0.2494 2848 -
obs--99.88 %

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