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- PDB-6tl7: CRYSTAL STRUCTURE OF LECTIN-LIKE OX-LDL RECEPTOR 1 (P212121) -

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Basic information

Entry
Database: PDB / ID: 6tl7
TitleCRYSTAL STRUCTURE OF LECTIN-LIKE OX-LDL RECEPTOR 1 (P212121)
ComponentsOxidized low-density lipoprotein receptor 1
KeywordsLIPID BINDING PROTEIN / LOX-1 / OLR1 / CTLD / C-TYPE LECTIN LIKE DOMAIN / SCAVENGER RECEPTOR / OXLDL BINDING
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 / 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
Similarity search - Domain/homology
NICKEL (II) ION / Oxidized low-density lipoprotein receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å
AuthorsNar, H. / Fiegen, D. / Schnapp, G.
CitationJournal: Commun Chem / Year: 2020
Title: A small-molecule inhibitor of lectin-like oxidized LDL receptor-1 acts by stabilizing an inactive receptor tetramer state
Authors: Nar, H. / Fiegen, D. / Schnapp, G.
History
DepositionDec 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidized low-density lipoprotein receptor 1
B: Oxidized low-density lipoprotein receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8764
Polymers30,7592
Non-polymers1172
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-30 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.490, 64.700, 101.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Oxidized low-density lipoprotein receptor 1 / Ox-LDL receptor 1 / C-type lectin domain family 8 member A / Lectin-like oxidized LDL receptor 1 / ...Ox-LDL receptor 1 / C-type lectin domain family 8 member A / Lectin-like oxidized LDL receptor 1 / hLOX-1 / Lectin-type oxidized LDL receptor 1


Mass: 15379.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OLR1, CLEC8A, LOX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P78380
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 2000MME, 0.15M KBr, pH 6.4-7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.11→101.85 Å / Num. obs: 94380 / % possible obs: 88.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 10.69 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.055 / Rrim(I) all: 0.055 / Net I/σ(I): 18.9
Reflection shellResolution: 1.11→1.17 Å / Rmerge(I) obs: 0.412 / Num. unique obs: 7658 / Rpim(I) all: 0.282 / Rrim(I) all: 0.505

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
BUSTER-TNTrefinement
SCALAdata scaling
Cootmodel building
autoPROCdata processing
XDSdata processing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ypu

1ypu


Resolution: 1.11→34.32 Å / SU ML: 0.0776 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.3482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1618 1898 2.01 %
Rwork0.1319 92408 -
obs0.1325 94306 88.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.35 Å2
Refinement stepCycle: LAST / Resolution: 1.11→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 2 509 2667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01092470
X-RAY DIFFRACTIONf_angle_d1.24943385
X-RAY DIFFRACTIONf_chiral_restr0.1005334
X-RAY DIFFRACTIONf_plane_restr0.0102451
X-RAY DIFFRACTIONf_dihedral_angle_d15.2257346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.11-1.140.2405800.22483099X-RAY DIFFRACTION42.16
1.14-1.170.2051900.18354191X-RAY DIFFRACTION56.95
1.17-1.20.18021070.15645109X-RAY DIFFRACTION69.31
1.2-1.240.19321180.14386480X-RAY DIFFRACTION87.69
1.24-1.280.18031360.12727158X-RAY DIFFRACTION96.62
1.28-1.340.17271670.11887187X-RAY DIFFRACTION97.22
1.34-1.40.15821290.11267219X-RAY DIFFRACTION97.03
1.4-1.470.14361230.10197299X-RAY DIFFRACTION98.14
1.47-1.560.13461590.10187281X-RAY DIFFRACTION97.88
1.56-1.680.1391410.10797332X-RAY DIFFRACTION98.19
1.68-1.850.14411340.12017410X-RAY DIFFRACTION98.73
1.85-2.120.14531720.12157406X-RAY DIFFRACTION98.68
2.12-2.670.15071640.14217494X-RAY DIFFRACTION99.27
2.67-34.320.17851780.14457743X-RAY DIFFRACTION98.56

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