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- PDB-8h24: Leucine-rich alpha-2-glycoprotein 1 -

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Basic information

Entry
Database: PDB / ID: 8h24
TitleLeucine-rich alpha-2-glycoprotein 1
ComponentsLeucine-rich alpha-2-glycoprotein
KeywordsUNKNOWN FUNCTION / Angiogenesis / Neurite outgrowth / soluble ligand / Secreted glycoprotein
Function / homology
Function and homology information


leukocyte adhesion to vascular endothelial cell / keratinocyte migration / positive regulation of keratinocyte proliferation / positive regulation of epithelial cell proliferation involved in wound healing / type II transforming growth factor beta receptor binding / type I transforming growth factor beta receptor binding / wound healing, spreading of epidermal cells / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of epithelial to mesenchymal transition / brown fat cell differentiation ...leukocyte adhesion to vascular endothelial cell / keratinocyte migration / positive regulation of keratinocyte proliferation / positive regulation of epithelial cell proliferation involved in wound healing / type II transforming growth factor beta receptor binding / type I transforming growth factor beta receptor binding / wound healing, spreading of epidermal cells / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of epithelial to mesenchymal transition / brown fat cell differentiation / positive regulation of endothelial cell proliferation / response to bacterium / specific granule lumen / positive regulation of angiogenesis / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane
Similarity search - Function
Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Leucine-rich alpha-2-glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsWon, S.Y. / Park, B.S. / Lee, D.S. / Kim, H.M. / Han, A. / Yang, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other governmentIBS-R030-C1 Korea, Republic Of
CitationJournal: Exp.Mol.Med. / Year: 2023
Title: Crystal structure of LRG1 and the functional significance of LRG1 glycan for LPHN2 activation.
Authors: Yang, J. / Yin, G.N. / Kim, D.K. / Han, A.R. / Lee, D.S. / Min, K.W. / Fu, Y. / Yun, J. / Suh, J.K. / Ryu, J.K. / Kim, H.M.
History
DepositionOct 4, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine-rich alpha-2-glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1986
Polymers38,2171
Non-polymers9815
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.018, 143.018, 113.728
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-545-

HOH

21A-589-

HOH

31A-655-

HOH

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Components

#1: Protein Leucine-rich alpha-2-glycoprotein / LRG


Mass: 38216.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRG1, LRG / Cell (production host): Freestyle293F / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P02750
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.39 Å3/Da / Density % sol: 71.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 200mM lithium sulfate, 100mM sodium acetate pH4.5, 48% PEG 400 (v/v)
PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 25623 / % possible obs: 99.9 % / Redundancy: 40 % / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.028 / Rrim(I) all: 0.177 / Χ2: 0.853 / Net I/σ(I): 4.4 / Num. measured all: 1025968
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.54390.7925030.9650.1270.80.634100
2.54-2.6439.50.66725210.9750.1070.6750.649100
2.64-2.76400.52725010.9860.0840.5330.666100
2.76-2.9400.43125220.9910.0690.4370.695100
2.9-3.0940.40.34625260.9940.0550.350.731100
3.09-3.3241.20.23425410.9970.0370.2370.804100
3.32-3.6641.40.15225600.9980.0240.1540.917100
3.66-4.19410.10525730.9990.0160.1061.063100
4.19-5.2840.50.08426110.9990.0130.0851.165100
5.28-5037.40.07527650.9990.0130.0761.16799.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NGL3, 3ZYN

3zyn


Resolution: 2.45→30.27 Å / SU ML: 0.2042 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.7342
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2194 2000 7.81 %
Rwork0.1857 23602 -
obs0.1885 25602 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.57 Å2
Refinement stepCycle: LAST / Resolution: 2.45→30.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 61 176 2635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862509
X-RAY DIFFRACTIONf_angle_d1.20373414
X-RAY DIFFRACTIONf_chiral_restr0.0766399
X-RAY DIFFRACTIONf_plane_restr0.0074448
X-RAY DIFFRACTIONf_dihedral_angle_d11.06061492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.520.23261390.19861636X-RAY DIFFRACTION99.78
2.52-2.580.26191410.19861665X-RAY DIFFRACTION100
2.58-2.660.27431390.20321635X-RAY DIFFRACTION100
2.66-2.750.24621400.19921657X-RAY DIFFRACTION100
2.75-2.840.24451410.19211662X-RAY DIFFRACTION100
2.84-2.960.22781400.19641660X-RAY DIFFRACTION100
2.96-3.090.24111410.19771663X-RAY DIFFRACTION100
3.09-3.250.23931420.19621672X-RAY DIFFRACTION100
3.25-3.460.20061420.19151681X-RAY DIFFRACTION100
3.46-3.720.20621420.16291673X-RAY DIFFRACTION100
3.72-4.10.19191440.15781693X-RAY DIFFRACTION100
4.1-4.690.19591450.15691716X-RAY DIFFRACTION100
4.69-5.90.22861480.18051738X-RAY DIFFRACTION100
5.9-30.270.21041560.22571851X-RAY DIFFRACTION100

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