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- PDB-7aae: Crystal structure of Human serum albumin in complex with myristic... -

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Basic information

Entry
Database: PDB / ID: 7aae
TitleCrystal structure of Human serum albumin in complex with myristic acid at 2.27 Angstrom Resolution
ComponentsAlbumin
KeywordsPROTEIN TRANSPORT / Serum protein / Lipid binding protein / Drug carrier
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
FORMIC ACID / MYRISTIC ACID / PHOSPHATE ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsMaso, L. / Liberi, S. / Trande, M. / Angelini, A. / Cendron, L.
CitationJournal: Protein Sci. / Year: 2021
Title: Unveiling the binding mode of perfluorooctanoic acid to human serum albumin.
Authors: Maso, L. / Trande, M. / Liberi, S. / Moro, G. / Daems, E. / Linciano, S. / Sobott, F. / Covaceuszach, S. / Cassetta, A. / Fasolato, S. / Moretto, L.M. / De Wael, K. / Cendron, L. / Angelini, A.
History
DepositionSep 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: 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 / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,55814
Polymers66,4561
Non-polymers2,10213
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-52 kcal/mol
Surface area28080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.315, 38.537, 184.280
Angle α, β, γ (deg.)90.000, 104.450, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Albumin


Mass: 66456.133 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

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Non-polymers , 5 types, 36 molecules

#2: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM HEPES, 50 mM MOPS, 30 mM sodium fluoride, 30 mM sodium bromide, 30 mM sodium iodide, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.27→29.23 Å / Num. obs: 30458 / % possible obs: 99.5 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.28
Reflection shellResolution: 2.27→2.35 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2962 / CC1/2: 0.866 / Rsym value: 0.583

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.12-2829refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bj5

1bj5


Resolution: 2.27→29.228 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.304 / WRfactor Rwork: 0.228 / Average fsc free: 0.8371 / Average fsc work: 0.8688 / Cross valid method: FREE R-VALUE / ESU R: 0.361 / ESU R Free: 0.273
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2907 1502 4.931 %
Rwork0.2237 28956 -
all0.227 --
obs-30458 99.516 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 61.474 Å2
Baniso -1Baniso -2Baniso -3
1--0.101 Å20 Å2-0.054 Å2
2--0.131 Å2-0 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 2.27→29.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 144 23 4789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124883
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.6516571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0855584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85923.454249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.45615873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0921524
X-RAY DIFFRACTIONr_chiral_restr0.1090.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023610
X-RAY DIFFRACTIONr_nbd_refined0.2220.22139
X-RAY DIFFRACTIONr_nbtor_refined0.30.23313
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2115
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2240.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2680.22
X-RAY DIFFRACTIONr_mcbond_it4.5095.8452333
X-RAY DIFFRACTIONr_mcangle_it6.5998.752918
X-RAY DIFFRACTIONr_scbond_it4.8446.3452550
X-RAY DIFFRACTIONr_scangle_it7.4739.3043653
X-RAY DIFFRACTIONr_lrange_it10.06179.5117067
LS refinement shellResolution: 2.27→2.329 Å
RfactorNum. reflection% reflection
Rfree0.378 125 -
Rwork0.289 2040 -
obs--99.8156 %

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