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- PDB-8itr: Crystal structure of lysophosphatidylcholine in complex with huma... -

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Basic information

Entry
Database: PDB / ID: 8itr
TitleCrystal structure of lysophosphatidylcholine in complex with human serum albumin
ComponentsAlbumin
KeywordsSTRUCTURAL PROTEIN / lysophosphatidylcholine / human serum albumin
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin
Similarity search - Domain/homology
[1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsWang, Y. / Jiang, L.G. / Huang, M.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biophys.J. / Year: 2023
Title: Crystal structures of human serum albumin in complex with lysophosphatidylcholine.
Authors: Wang, Y. / Luo, Z. / Morelli, X. / Xu, P. / Jiang, L. / Shi, X. / Huang, M.
History
DepositionMar 22, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0837
Polymers66,2721
Non-polymers2,8126
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-12 kcal/mol
Surface area29980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.729, 38.843, 95.186
Angle α, β, γ (deg.)90.00, 105.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Albumin /


Mass: 66271.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Komagataella pastoris (fungus) / References: UniProt: P02768
#2: Chemical
ChemComp-LPC / [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE


Mass: 468.585 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H47NO7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) polyethylene glycol 3350 in 50 mM potassium phosphate, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 258740 / % possible obs: 98.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 37.3
Reflection shellResolution: 2.44→2.5 Å / Rmerge(I) obs: 0.251 / Num. unique obs: 1152

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→46.02 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2735974.42 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 2394 9.9 %RANDOM
Rwork0.255 ---
obs0.255 24162 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.8069 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 69.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å26.16 Å2
2--21.16 Å20 Å2
3----21.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.28 Å
Refinement stepCycle: 1 / Resolution: 2.44→46.02 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 0 0
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.44→2.59 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 341 9.6 %
Rwork0.293 3204 -
obs--86.5 %

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