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- PDB-5a2e: Extracellular SRCR domains of human CD6 -

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Basic information

Entry
Database: PDB / ID: 5a2e
TitleExtracellular SRCR domains of human CD6
ComponentsT-CELL DIFFERENTIATION ANTIGEN CD6
KeywordsIMMUNE SYSTEM / SCAVENGER RECEPTOR CYSTEINE RICH / SRCR
Function / homology
Function and homology information


: / lipoteichoic acid binding / acute inflammatory response to antigenic stimulus / immunological synapse formation / scavenger receptor activity / positive regulation of cytokine production involved in inflammatory response / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / plasma membrane => GO:0005886 / immunological synapse / positive regulation of T cell proliferation ...: / lipoteichoic acid binding / acute inflammatory response to antigenic stimulus / immunological synapse formation / scavenger receptor activity / positive regulation of cytokine production involved in inflammatory response / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / plasma membrane => GO:0005886 / immunological synapse / positive regulation of T cell proliferation / lipopolysaccharide-mediated signaling pathway / lipopolysaccharide binding / adaptive immune response / response to lipopolysaccharide / external side of plasma membrane / innate immune response / extracellular region / identical protein binding
Similarity search - Function
Mac-2 Binding Protein / SRCR-like domain / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Roll / Alpha Beta
Similarity search - Domain/homology
T-cell differentiation antigen CD6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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

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Assembly

Deposited unit
A: T-CELL DIFFERENTIATION ANTIGEN CD6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2078
Polymers39,6131
Non-polymers5947
Water77543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.480, 161.480, 93.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein T-CELL DIFFERENTIATION ANTIGEN CD6 / T12 / TP120 / HUMAN CD6


Mass: 39613.168 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR SRCR 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: P30203
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 5.46 Å3/Da / Density % sol: 77.49 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M AMMONIUM SULFATE, 0.3M SODIUM FORMATE, 0.1M SODIUM CACODYLATE, 3% W/V PGA-LM, 20% MPD, PH 6.5

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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: Jan 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.15→77.93 Å / Num. obs: 12884 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 71.97 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 7.2
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BY2

1by2


Resolution: 3.15→77.93 Å / Cor.coef. Fo:Fc: 0.8352 / Cor.coef. Fo:Fc free: 0.7738 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.715 / SU Rfree Blow DPI: 0.384
RfactorNum. reflection% reflectionSelection details
Rfree0.2831 629 4.88 %RANDOM
Rwork0.2531 ---
obs0.2545 12883 99.34 %-
Displacement parametersBiso mean: 37.69 Å2
Baniso -1Baniso -2Baniso -3
1--3.5678 Å20 Å20 Å2
2---3.5678 Å20 Å2
3---7.1357 Å2
Refine analyzeLuzzati coordinate error obs: 0.731 Å
Refinement stepCycle: LAST / Resolution: 3.15→77.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 38 43 2341
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0064549HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.768155HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d968SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes736HARMONIC5
X-RAY DIFFRACTIONt_it4549HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.74
X-RAY DIFFRACTIONt_other_torsion13.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion286SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4423SEMIHARMONIC4
LS refinement shellResolution: 3.15→3.45 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3076 156 5.19 %
Rwork0.2848 2851 -
all0.286 3007 -
obs--99.34 %

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