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- PDB-4ety: Crystal structure of a strand-swapped dimer of Mouse Leukocyte-as... -

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Basic information

Entry
Database: PDB / ID: 4ety
TitleCrystal structure of a strand-swapped dimer of Mouse Leukocyte-associated immunoglobulin-like receptor 1 (NYSGRC-006047) Extra Cellular Domain
ComponentsLeukocyte-associated immunoglobulin-like receptor 1
KeywordsIMMUNE SYSTEM / LAIR-1 / IG-like domain / Extra Celluar Domain / Domain swapping / NYSGRC / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / Collagen Receptor / Collagen / Atoms-to-Animals: The Immune Function Network / IFN
Function / homology
Function and homology information


Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / plasma membrane
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Leukocyte-associated immunoglobulin-like receptor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSampathkumar, P. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: to be published
Title: Crystal structure of a strand-swapped dimer of Mouse Leukocyte-associated immunoglobulin-like receptor 1 Extra Cellular Domain
Authors: Sampathkumar, P. / Ramagopal, U.A. / Bonanno, J. / Fiser, A. / Zencheck, W. / Nathenson, S.G. / Almo, S.C.
History
DepositionApr 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leukocyte-associated immunoglobulin-like receptor 1
B: Leukocyte-associated immunoglobulin-like receptor 1
C: Leukocyte-associated immunoglobulin-like receptor 1
D: Leukocyte-associated immunoglobulin-like receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,21814
Polymers53,5984
Non-polymers62110
Water1,69394
1
A: Leukocyte-associated immunoglobulin-like receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5243
Polymers13,3991
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leukocyte-associated immunoglobulin-like receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6485
Polymers13,3991
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Leukocyte-associated immunoglobulin-like receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4612
Polymers13,3991
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Leukocyte-associated immunoglobulin-like receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5864
Polymers13,3991
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-44 kcal/mol
Surface area16660 Å2
MethodPISA
6
A: Leukocyte-associated immunoglobulin-like receptor 1
C: Leukocyte-associated immunoglobulin-like receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9855
Polymers26,7992
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-18 kcal/mol
Surface area11030 Å2
MethodPISA
7
B: Leukocyte-associated immunoglobulin-like receptor 1
D: Leukocyte-associated immunoglobulin-like receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2339
Polymers26,7992
Non-polymers4347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-10 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.588, 57.427, 47.795
Angle α, β, γ (deg.)90.000, 105.150, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Leukocyte-associated immunoglobulin-like receptor 1 / LAIR-1 / mLAIR1


Mass: 13399.379 Da / Num. of mol.: 4 / Fragment: Extra Cellular Domain (UNP Residues 22-133)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lair1 / Plasmid: pNIC28-Bas4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus RIL / References: UniProt: Q8BG84
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 5.5
Details: Protein preparation by Refolding. Protein (11.5mg/ml in 20 mM Trizma Base pH 8.0, 100 mM NaCl; Reservoir ( 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350; ...Details: Protein preparation by Refolding. Protein (11.5mg/ml in 20 mM Trizma Base pH 8.0, 100 mM NaCl; Reservoir ( 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350; Index HR F10); Cryoprotection (30% Ethylene glycol in Reservior solution), Sitting Drop Vapor Diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 21, 2011 / Details: MIRRORS
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 36280 / Num. obs: 36066 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.103 / Net I/σ(I): 13.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.8 % / Num. unique all: 1742 / Rsym value: 0.946 / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0025refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: Built using Phenix AutoSol wizard

Resolution: 1.9→27.81 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.053 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 1798 5 %RANDOM
Rwork0.2003 ---
obs0.2017 36066 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.71 Å2 / Biso mean: 33.5637 Å2 / Biso min: 16.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20.17 Å2
2--2.39 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 40 94 3127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023129
X-RAY DIFFRACTIONr_bond_other_d0.0020.022916
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9864235
X-RAY DIFFRACTIONr_angle_other_deg0.7813.0026763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7195396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15924.746118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43115507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.486158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02644
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 125 -
Rwork0.23 2416 -
all-2541 -
obs--95.78 %

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