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- PDB-9jdo: LCN2 in complex with phosphoserine -

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Basic information

Entry
Database: PDB / ID: 9jdo
TitleLCN2 in complex with phosphoserine
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / Metal sequestration by antimicrobial proteins / siderophore transport / response to kainic acid / response to mycotoxin / response to blue light ...positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / Metal sequestration by antimicrobial proteins / siderophore transport / response to kainic acid / response to mycotoxin / response to blue light / cellular response to increased oxygen levels / response to fructose / cellular response to X-ray / short-term memory / cellular response to interleukin-6 / iron ion sequestering activity / enterobactin binding / response to herbicide / response to iron(II) ion / positive regulation of reactive oxygen species biosynthetic process / cellular response to interleukin-1 / long-term memory / cellular response to nutrient levels / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of endothelial cell migration / Iron uptake and transport / acute-phase response / cellular response to nerve growth factor stimulus / response to virus / specific granule lumen / cellular response to hydrogen peroxide / cellular response to amyloid-beta / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / cellular response to lipopolysaccharide / protease binding / Interleukin-4 and Interleukin-13 signaling / cellular response to hypoxia / defense response to bacterium / iron ion binding / response to xenobiotic stimulus / innate immune response / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin signature.
Similarity search - Domain/homology
PHOSPHOSERINE / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsQin, J. / Hu, X. / Wang, L. / Wei, H.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Targeting LCN2 breaks the phosphatidylserine-rich niches to restore NK cells anti-tumor immunity
Authors: Qin, J. / Hu, X. / Wang, L. / Wei, H.
History
DepositionAug 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7582
Polymers20,5731
Non-polymers1851
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)53.107, 53.107, 126.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Neutrophil gelatinase-associated lipocalin / NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / Siderocalin / p25


Mass: 20572.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Production host: Escherichia coli (E. coli) / References: UniProt: P80188
#2: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8NO6P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Tris-Hcl pH 7.9, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.85→48.95 Å / Num. obs: 4674 / % possible obs: 100 % / Redundancy: 16.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.026 / Rrim(I) all: 0.108 / Χ2: 0.99 / Net I/σ(I): 23.4 / Num. measured all: 76437
Reflection shellResolution: 2.85→3 Å / % possible obs: 100 % / Redundancy: 17.8 % / Rmerge(I) obs: 1.329 / Num. measured all: 11799 / Num. unique obs: 662 / CC1/2: 0.803 / Rpim(I) all: 0.319 / Rrim(I) all: 1.368 / Χ2: 0.99 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→48.95 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2857 236 5.09 %
Rwork0.2331 --
obs0.2362 4634 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1369 0 11 0 1380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031416
X-RAY DIFFRACTIONf_angle_d0.6171927
X-RAY DIFFRACTIONf_dihedral_angle_d19.691512
X-RAY DIFFRACTIONf_chiral_restr0.046210
X-RAY DIFFRACTIONf_plane_restr0.006248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.590.38271020.26912150X-RAY DIFFRACTION100
3.59-48.950.26321340.22162248X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -14.336 Å / Origin y: 11.061 Å / Origin z: -1.736 Å
111213212223313233
T0.3072 Å20.107 Å20.0056 Å2-0.3762 Å2-0.0413 Å2--0.3545 Å2
L1.3223 °20.6267 °2-0.0203 °2-1.4205 °2-0.172 °2--1.6551 °2
S-0.087 Å °-0.0698 Å °0.3111 Å °-0.0556 Å °0.1517 Å °-0.4112 Å °0.1818 Å °-0.2942 Å °0 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 26:177 )

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