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- PDB-8hna: Crystal structure of N-terminal fragment (20-221aa) of human SCARF1 -

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Basic information

Entry
Database: PDB / ID: 8hna
TitleCrystal structure of N-terminal fragment (20-221aa) of human SCARF1
ComponentsScavenger receptor class F member 1
KeywordsLIPID BINDING PROTEIN / Cell surface receptor
Function / homology
Function and homology information


low-density lipoprotein particle binding / scavenger receptor activity / cholesterol catabolic process / Scavenging by Class F Receptors / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / neuron remodeling / positive regulation of axon regeneration / dendrite development / receptor-mediated endocytosis / positive regulation of neuron projection development ...low-density lipoprotein particle binding / scavenger receptor activity / cholesterol catabolic process / Scavenging by Class F Receptors / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / neuron remodeling / positive regulation of axon regeneration / dendrite development / receptor-mediated endocytosis / positive regulation of neuron projection development / endocytic vesicle membrane / transmembrane signaling receptor activity / membrane / plasma membrane
Similarity search - Function
Scavenger receptor class F member SREC1/2 / Laminin EGF domain / Laminin-type EGF domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Scavenger receptor class F member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, Y. / He, Y. / Li, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No.91957102 China
CitationJournal: To Be Published
Title: Crystal structure of N-terminal of SCARF1 at 2.6 Angstroms resolution
Authors: Wang, Y. / He, Y.
History
DepositionDec 7, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Scavenger receptor class F member 1


Theoretical massNumber of molelcules
Total (without water)23,0421
Polymers23,0421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.007, 102.007, 83.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Scavenger receptor class F member 1 / Acetyl LDL receptor / Scavenger receptor expressed by endothelial cells 1 / SREC-I


Mass: 23042.059 Da / Num. of mol.: 1 / Fragment: N-terminal 20-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCARF1, KIAA0149, SREC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q14162
Has protein modificationY

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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: 4.72 Å3/Da / Density % sol: 73.94 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M citric acid/sodium citrate (pH 3.6), 9% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 14015 / % possible obs: 99.1 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 32.125
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.78 / Num. unique obs: 1299

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.18.2-3874-000refinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→26.89 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 1397 10.01 %
Rwork0.2288 --
obs0.2305 13959 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→26.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 0 0 1133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071170
X-RAY DIFFRACTIONf_angle_d1.0681586
X-RAY DIFFRACTIONf_dihedral_angle_d15.219166
X-RAY DIFFRACTIONf_chiral_restr0.048145
X-RAY DIFFRACTIONf_plane_restr0.007221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.34781300.33971167X-RAY DIFFRACTION93
2.69-2.80.33051350.30331212X-RAY DIFFRACTION99
2.8-2.930.31131380.27611242X-RAY DIFFRACTION100
2.93-3.080.29961390.29241247X-RAY DIFFRACTION100
3.08-3.270.3331380.26331245X-RAY DIFFRACTION100
3.27-3.530.26131400.25631254X-RAY DIFFRACTION100
3.53-3.880.22841400.2081259X-RAY DIFFRACTION100
3.88-4.440.23741420.18361277X-RAY DIFFRACTION100
4.44-5.590.18981440.18751293X-RAY DIFFRACTION100
5.59-26.890.24641510.24811366X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 22.9095 Å / Origin y: 82.6801 Å / Origin z: 36.7246 Å
111213212223313233
T0.7319 Å2-0.0405 Å20.0472 Å2-0.7697 Å2-0.0416 Å2--0.6587 Å2
L3.1721 °2-0.0333 °20.3624 °2-0.0691 °2-0.0778 °2--0.0108 °2
S0.176 Å °0.21 Å °0.1896 Å °-0.1733 Å °-0.1451 Å °0.017 Å °0.0234 Å °0.1807 Å °-0.0388 Å °
Refinement TLS groupSelection details: all

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