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- PDB-1ypo: Human Oxidized Low Density Lipoprotein Receptor LOX-1 P3 1 21 Spa... -

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Basic information

Entry
Database: PDB / ID: 1ypo
TitleHuman Oxidized Low Density Lipoprotein Receptor LOX-1 P3 1 21 Space Group
Componentsoxidised low density lipoprotein (lectin-like) receptor 1
KeywordsIMMUNE SYSTEM / Oxidized Low Density Lipoprotein receptor / Lox-1 / CTLD / C-type lectin like domain / NK Cell receptor
Function / homology
Function and homology information


low-density lipoprotein particle receptor activity / lipoprotein metabolic process / blood circulation / leukocyte cell-cell adhesion / immune system process / tertiary granule membrane / specific granule membrane / Cell surface interactions at the vascular wall / carbohydrate binding / receptor complex ...low-density lipoprotein particle receptor activity / lipoprotein metabolic process / blood circulation / leukocyte cell-cell adhesion / immune system process / tertiary granule membrane / specific granule membrane / Cell surface interactions at the vascular wall / carbohydrate binding / receptor complex / inflammatory response / membrane raft / intracellular membrane-bounded organelle / Neutrophil degranulation / proteolysis / extracellular region / nucleoplasm / membrane / identical protein binding / plasma membrane
Similarity search - Function
Ly49-like, N-terminal / Ly49-like protein, N-terminal region / Natural killer cell receptor-like, C-type lectin-like domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily ...Ly49-like, N-terminal / Ly49-like protein, N-terminal region / Natural killer cell receptor-like, C-type lectin-like domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Oxidized low-density lipoprotein receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPark, H. / Adsit, F.G. / Boyington, J.C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The 1.4 angstrom crystal structure of the human oxidized low density lipoprotein receptor lox-1.
Authors: Park, H. / Adsit, F.G. / Boyington, J.C.
History
DepositionJan 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: oxidised low density lipoprotein (lectin-like) receptor 1
B: oxidised low density lipoprotein (lectin-like) receptor 1
C: oxidised low density lipoprotein (lectin-like) receptor 1
D: oxidised low density lipoprotein (lectin-like) receptor 1
E: oxidised low density lipoprotein (lectin-like) receptor 1
F: oxidised low density lipoprotein (lectin-like) receptor 1
G: oxidised low density lipoprotein (lectin-like) receptor 1
H: oxidised low density lipoprotein (lectin-like) receptor 1


Theoretical massNumber of molelcules
Total (without water)120,3218
Polymers120,3218
Non-polymers00
Water0
1
A: oxidised low density lipoprotein (lectin-like) receptor 1
B: oxidised low density lipoprotein (lectin-like) receptor 1


Theoretical massNumber of molelcules
Total (without water)30,0802
Polymers30,0802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-8 kcal/mol
Surface area13430 Å2
MethodPISA
2
C: oxidised low density lipoprotein (lectin-like) receptor 1
D: oxidised low density lipoprotein (lectin-like) receptor 1


Theoretical massNumber of molelcules
Total (without water)30,0802
Polymers30,0802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-10 kcal/mol
Surface area12940 Å2
MethodPISA
3
E: oxidised low density lipoprotein (lectin-like) receptor 1
F: oxidised low density lipoprotein (lectin-like) receptor 1


Theoretical massNumber of molelcules
Total (without water)30,0802
Polymers30,0802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-10 kcal/mol
Surface area12840 Å2
MethodPISA
4
G: oxidised low density lipoprotein (lectin-like) receptor 1
H: oxidised low density lipoprotein (lectin-like) receptor 1


Theoretical massNumber of molelcules
Total (without water)30,0802
Polymers30,0802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-8 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.7, 97.7, 215.1
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer (chain A and B)

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Components

#1: Protein
oxidised low density lipoprotein (lectin-like) receptor 1


Mass: 15040.122 Da / Num. of mol.: 8 / Fragment: C-type lectin-like domain (Residues 142-273)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P78380

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 277 K / pH: 5.5
Details: ammonium acetate, Bis-Tris, PEG 10K, HEPES, NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 1, 2004 / Details: OSMIC MIRROR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 24056 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rsym value: 0.101 / Net I/σ(I): 22
Reflection shellResolution: 3→3.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.532 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YPQ

1ypq


Resolution: 3→10 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 153980.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1064 5 %RANDOM
Rwork0.228 ---
obs0.228 22145 93.1 %-
all-23784 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.6771 Å2 / ksol: 0.385831 e/Å3
Displacement parametersBiso mean: 46.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8363 0 0 0 8363
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.18 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 139 4.1 %
Rwork0.313 3272 -
obs--87.3 %

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