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- PDB-7xmp: High resolution structure of lectin-like Ox-LDL receptor 1 in spa... -

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Basic information

Entry
Database: PDB / ID: 7xmp
TitleHigh resolution structure of lectin-like Ox-LDL receptor 1 in space group P 32 2 1
ComponentsOxidized low-density lipoprotein receptor 1
KeywordsLIPID BINDING PROTEIN / Lectin-like OxLDL Receptor 1 / OLR1 / native / CLEC8A
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 / identical protein binding / membrane / 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: 1.27 Å
AuthorsTomar, A. / Varughese, K.I. / Arockiasamy, A.
Funding support India, 2items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)09/512(0221)/2016 India
Department of Science & Technology (DST, India)EMR/2017/00506 India
CitationJournal: To Be Published
Title: High resolution structure of lectin like Ox-LDL receptor 1 in space group P 32 2 1
Authors: Tomar, A. / Arockiasamy, A. / Varughese, K.I.
History
DepositionApr 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: 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


Theoretical massNumber of molelcules
Total (without water)15,6691
Polymers15,6691
Non-polymers00
Water2,198122
1
A: Oxidized low-density lipoprotein receptor 1

A: Oxidized low-density lipoprotein receptor 1


Theoretical massNumber of molelcules
Total (without water)31,3382
Polymers31,3382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area1560 Å2
ΔGint-8 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.030, 50.030, 91.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OLR1, CLEC8A, LOX1 / Production host: Escherichia coli B (bacteria) / References: UniProt: P78380
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2M ammonium sulfate, 0.2 M sodium chloride, 0.1M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.257→43.33 Å / Num. obs: 36626 / % possible obs: 99.5 % / Redundancy: 16.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.025 / Rrim(I) all: 0.101 / Net I/σ(I): 15.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.257-1.2816.91.6413099518330.7020.4051.6921.896.6
3.523-43.32714.60.0712666218320.9970.0180.07432.299.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDS20210205data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YPU

1ypu


Resolution: 1.27→43.33 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.513 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 1741 4.9 %RANDOM
Rwork0.1578 ---
obs0.1598 33554 99.65 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 67.15 Å2 / Biso mean: 19.071 Å2 / Biso min: 8.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å2-0 Å2
2---0.38 Å20 Å2
3---1.23 Å2
Refinement stepCycle: final / Resolution: 1.27→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 0 122 1148
Biso mean---30.29 -
Num. residues----128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0181076
X-RAY DIFFRACTIONr_bond_other_d0.0020.019958
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.8331465
X-RAY DIFFRACTIONr_angle_other_deg1.1742.6862210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1465128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93822.36455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.26215166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.464155
X-RAY DIFFRACTIONr_chiral_restr0.1070.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021227
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02275
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.76832034
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.274→1.307 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 101 -
Rwork0.282 2444 -
all-2545 -
obs--98.91 %

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