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- PDB-2d3v: Crystal Structure of Leukocyte Ig-like Receptor A5 (LILRA5/LIR9/ILT11) -

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Basic information

Entry
Database: PDB / ID: 2d3v
TitleCrystal Structure of Leukocyte Ig-like Receptor A5 (LILRA5/LIR9/ILT11)
Componentsleukocyte immunoglobulin-like receptor subfamily A member 5 isoform 1
KeywordsIMMUNE SYSTEM / Immunoglobulin-like fold
Function / homology
Function and homology information


positive regulation of cell activation / positive regulation of tumor necrosis factor production => GO:0032760 / negative regulation of interleukin-13 production / negative regulation of interleukin-12 production / positive regulation of calcium ion transport / positive regulation of interleukin-10 production / positive regulation of protein tyrosine kinase activity / positive regulation of interleukin-1 beta production / positive regulation of inflammatory response / positive regulation of interleukin-6 production ...positive regulation of cell activation / positive regulation of tumor necrosis factor production => GO:0032760 / negative regulation of interleukin-13 production / negative regulation of interleukin-12 production / positive regulation of calcium ion transport / positive regulation of interleukin-10 production / positive regulation of protein tyrosine kinase activity / positive regulation of interleukin-1 beta production / positive regulation of inflammatory response / positive regulation of interleukin-6 production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of MAPK cascade / membrane => GO:0016020 / innate immune response / cell surface / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Leukocyte immunoglobulin-like receptor subfamily A member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsShiroishi, M. / Kajikawa, M. / Kuroki, K. / Ose, T. / Kohda, D. / Maenaka, K.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal structure of the human monocyte-activating receptor,
Authors: Shiroishi, M. / Kajikawa, M. / Kuroki, K. / Ose, T. / Kohda, D. / Maenaka, K.
History
DepositionOct 3, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: leukocyte immunoglobulin-like receptor subfamily A member 5 isoform 1


Theoretical massNumber of molelcules
Total (without water)22,1241
Polymers22,1241
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.080, 58.645, 131.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein leukocyte immunoglobulin-like receptor subfamily A member 5 isoform 1 / Leukocyte Ig-like Receptor A5 (LILRA5/LIR9/ILT11)


Mass: 22123.561 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 32490553, UniProt: A6NI73*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.5 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Bicine, PEG20000, Dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97921, 0.97956, 0.90000, 1.0000
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979561
30.91
411
ReflectionResolution: 1.8→50 Å / Num. obs: 19328 / % possible obs: 92.1 % / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1011 / % possible all: 49.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / SU B: 3.364 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.163 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The structure was refined also with CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26861 951 5.1 %RANDOM
Rwork0.23363 ---
obs0.23547 17645 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.844 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20 Å2
2--0.4 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 0 105 1541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221481
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9612018
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2725176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14422.57666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48115238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8641513
X-RAY DIFFRACTIONr_chiral_restr0.1020.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021139
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.2563
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2962
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0461.5922
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70121460
X-RAY DIFFRACTIONr_scbond_it2.3073652
X-RAY DIFFRACTIONr_scangle_it3.4934.5558
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 42 -
Rwork0.297 910 -
obs-952 67.04 %

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