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- PDB-7z57: Crystal structure of Human Serum Albumin in complex with surfacta... -

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Basic information

Entry
Database: PDB / ID: 7z57
TitleCrystal structure of Human Serum Albumin in complex with surfactant GenX (2,3,3,3-tetrafluoro-2-(heptafluoropropoxy) propanoate)
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / serum albumin / lipid binder
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 / small molecule 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
BROMIDE ION / Chem-IGB / MYRISTIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiberi, S. / Moro, G. / Vascon, F. / Linciano, S. / De Toni, L. / Angelin, A. / Cendron, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca Italy
CitationJournal: Chem.Res.Toxicol. / Year: 2022
Title: Investigation of the Interaction between Human Serum Albumin and Branched Short-Chain Perfluoroalkyl Compounds.
Authors: Moro, G. / Liberi, S. / Vascon, F. / Linciano, S. / De Felice, S. / Fasolato, S. / Foresta, C. / De Toni, L. / Di Nisio, A. / Cendron, L. / Angelini, A.
History
DepositionMar 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,81914
Polymers66,4561
Non-polymers2,36313
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-70 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.890, 38.769, 96.446
Angle α, β, γ (deg.)90.000, 105.000, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Albumin /


Mass: 66456.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MISSING RESIDUES ARE NOT VISIBLE IN THE ELECTRON DENSITY MAPS
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

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Non-polymers , 5 types, 47 molecules

#2: Chemical ChemComp-IGB / (2R)-2,3,3,3-tetrakis(fluoranyl)-2-[1,1,2,2,3,3,3-heptakis(fluoranyl)propoxy]propanoic acid / 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)propanoic acid / FRD-903


Mass: 330.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6HF11O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2
#5: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.53 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.09M Sodium fluoride; 0.09M Sodium bromide; 0.09M Sodium iodide; 12.5 % v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350; 0.05M Tris (base); 0.05M Bicine pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.2→93.16 Å / Num. obs: 34368 / % possible obs: 99.7 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.78 / Num. unique obs: 3431 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AAE

7aae


Resolution: 2.2→93.16 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.264 3448 -
Rwork0.237 --
obs-34368 99.7 %
Displacement parametersBiso max: 114.27 Å2 / Biso mean: 50.6636 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.2→93.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 157 34 4813

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