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- PDB-2ja4: Crystal structure of CD5 domain III reveals the fold of a group B... -

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Basic information

Entry
Database: PDB / ID: 2ja4
TitleCrystal structure of CD5 domain III reveals the fold of a group B scavenger cysteine-rich receptor
ComponentsT-CELL SURFACE GLYCOPROTEIN CD5
KeywordsIMMUNE SYSTEM / CD6 / CD5 / SRCR / MEMBRANE / POLYMORPHISM / GLYCOPROTEIN / TRANSMEMBRANE / INNATE IMMUNITY / PHOSPHORYLATION
Function / homology
Function and homology information


cell recognition / T cell costimulation / apoptotic signaling pathway / signaling receptor activity / external side of plasma membrane / plasma membrane
Similarity search - Function
T-cell surface glycoprotein CD5 / Mac-2 Binding Protein / SRCR-like domain / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Roll / Alpha Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å
AuthorsRodamilans, B. / Munoz, I.G. / Sarrias, M.R. / Lozano, F. / Blanco, F.J. / Montoya, G.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure of the Third Extracellular Domain of Cd5 Reveals the Fold of a Group B Scavenger Cysteine-Rich Receptor Domain.
Authors: Rodamilans, B. / Munoz, I.G. / Bragado-Nilsson, E. / Sarrias, M.R. / Padilla, O. / Blanco, F.J. / Lozano, F. / Montoya, G.
History
DepositionNov 21, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-CELL SURFACE GLYCOPROTEIN CD5


Theoretical massNumber of molelcules
Total (without water)11,3161
Polymers11,3161
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.931, 62.931, 72.564
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2045-

HOH

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Components

#1: Protein T-CELL SURFACE GLYCOPROTEIN CD5 / CD5DIII / LYMPHOCYTE ANTIGEN T1/LEU-1


Mass: 11315.667 Da / Num. of mol.: 1 / Fragment: DOMAIN III, RESIDUES 269-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-LYMPHOCYTE / Plasmid: PCEP-PU / Cell line (production host): HEK-293EBNA / Production host: HOMO SAPIENS (human) / Tissue (production host): KIDNEY CELLS / References: UniProt: P06127
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.7 Å3/Da / Density % sol: 67.4 %
Crystal growpH: 7.4 / Details: 15-25% PEG 8000, 100 MM NAAC PH 4.4, 200 MM LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.8
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 12098 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 2.21→2.26 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.2 / % possible all: 95.6

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Processing

Software
NameVersionClassification
ARP/wARPmodel building
SCALEPACKdata scaling
BNPphasing
SHARPphasing
SOLOMONphasing
ARP/wARPphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: SAD / Resolution: 2.21→19.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.474 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 387 4.7 %RANDOM
Rwork0.193 ---
obs0.196 7899 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.21→19.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms789 0 0 58 847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021808
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1561.9281093
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.5845100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04723.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.02615137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.84158
X-RAY DIFFRACTIONr_chiral_restr0.1830.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02623
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2590.2315
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.2540
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4921.5515
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.8632802
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.2413338
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.8234.5291
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.21→2.27 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.376 25
Rwork0.284 481

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