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- PDB-7w5d: High resolution structure of lectin-ike Ox-LDL Receptor 1 -

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Basic information

Entry
Database: PDB / ID: 7w5d
TitleHigh resolution structure of lectin-ike Ox-LDL Receptor 1
ComponentsOxidized low-density lipoprotein receptor 1
KeywordsLIPID BINDING PROTEIN / Lectin-like Ox-LDL receptor 1 / OLR1 / native
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
Oxidized low-density lipoprotein receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.141 Å
AuthorsTomar, A. / Arockiasamy, A.
Funding support India, 4items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)09/512(0221)/2016 India
Department of Biotechnology (DBT, India)BT/PR8766/BRB/10/1701/2018 India
Department of Science & Technology (DST, India)EMR/2017/005066 India
Department of Biotechnology (DBT, India)BT/PR28080/BID/7/836/2018 India
CitationJournal: To Be Published
Title: High Resolution Structure of Lectin-Like Ox-LDL Receptor 1
Authors: Tomar, A. / Arockiasamy, A.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)31,3382
Polymers31,3382
Non-polymers00
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-14 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.033, 49.726, 76.580
Angle α, β, γ (deg.)90.000, 98.570, 90.000
Int Tables number5
Space group name H-MC121

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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 / LOX-1 / Lectin-like oxLDL receptor 1 / hLOX-1 / Lectin-type oxidized LDL receptor 1


Mass: 15668.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OLR1, CLEC8A, LOX1 / Plasmid: pET-15b / Production host: Escherichia coli B (bacteria) / References: UniProt: P78380
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein 8mg/ml, 10mM Tris-HCl, 150mM NaCl, 1.1 M Sodium Malonate, 0.1M HEPES pH 7, 0.5% v/v Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.01→75.724 Å / Num. obs: 105602 / % possible obs: 91.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 12.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.025 / Rrim(I) all: 0.045 / Net I/σ(I): 12 / Num. measured all: 307143
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.9 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.01-1.0950.6011533352810.6270.4110.7321.659.8
2.97-75.7240.0231530552800.9980.0160.02840.194.4

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (16-JUL-2021)refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHASER2.8.3phasing
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YPQ

1ypq


Resolution: 1.141→16.62 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.038 / SU Rfree Blow DPI: 0.039 / SU Rfree Cruickshank DPI: 0.036
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 4681 5 %RANDOM
Rwork0.1802 ---
obs0.1809 93536 97.6 %-
Displacement parametersBiso max: 74.77 Å2 / Biso mean: 17.33 Å2 / Biso min: 7.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.5836 Å20 Å20.8317 Å2
2---1.0539 Å20 Å2
3---0.4703 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: final / Resolution: 1.141→16.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2121 0 0 369 2490
Biso mean---28.92 -
Num. residues----266
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d740SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes378HARMONIC5
X-RAY DIFFRACTIONt_it2246HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion278SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2384SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2246HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg3066HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion4.84
X-RAY DIFFRACTIONt_other_torsion14.94
LS refinement shellResolution: 1.141→1.15 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2268 102 5.45 %
Rwork0.2439 1769 -
obs--92.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4237-0.2043-0.150.51210.28580.45860.0013-0.0055-0.0195-0.01250.0077-0.0210.01280.0058-0.009-0.01270.0045-0.0016-0.0110.0022-0.002115.0037-08.5995
20.27510.20280.09281.08290.37660.5554-0.06450.011-0.00640.02080.03150.0509-0.05420.01330.03310.0026-0.0025-0.0063-0.00920.003-0.02274.900120.508126.9642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A140 - 270
2X-RAY DIFFRACTION2{ B|* }B136 - 270

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