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- PDB-6yg9: CRYSTAL STRUCTURE OF HUMAN SERUM ALBUMIN (HSA) IN COMPLEX WITH GN-07. -

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Basic information

Entry
Database: PDB / ID: 6yg9
TitleCRYSTAL STRUCTURE OF HUMAN SERUM ALBUMIN (HSA) IN COMPLEX WITH GN-07.
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / drug Transport / fatty acid binding / liver Imaging / NASH / 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 / 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
MYRISTIC ACID / Chem-OQ5 / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSchreuder, H.A. / Liesum, A.
CitationJournal: Adv Sci / Year: 2020
Title: Triantennary GalNAc Molecular Imaging Probes for Monitoring Hepatocyte Function in a Rat Model of Nonalcoholic Steatohepatitis.
Authors: Mishra, A. / Castaneda, T.R. / Bader, E. / Elshorst, B. / Cummings, S. / Scherer, P. / Bangari, D.S. / Loewe, C. / Schreuder, H. / Poverlein, C. / Helms, M. / Jones, S. / Zech, G. / Licher, ...Authors: Mishra, A. / Castaneda, T.R. / Bader, E. / Elshorst, B. / Cummings, S. / Scherer, P. / Bangari, D.S. / Loewe, C. / Schreuder, H. / Poverlein, C. / Helms, M. / Jones, S. / Zech, G. / Licher, T. / Wagner, M. / Schudok, M. / de Hoop, M. / Plowright, A.T. / Atzrodt, J. / Kannt, A. / Laitinen, I. / Derdau, V.
History
DepositionMar 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7598
Polymers66,5711
Non-polymers2,1877
Water11,926662
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint33 kcal/mol
Surface area28610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.722, 38.141, 95.372
Angle α, β, γ (deg.)90.000, 105.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1353-

HOH

21A-1354-

HOH

31A-1362-

HOH

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Components

#1: Protein Serum albumin


Mass: 66571.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768
#2: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-OQ5 / 20-[[(2~{S})-5-[2-[2-[2-[2-[2-[2-(diethylamino)-2-oxidanylidene-ethoxy]ethoxy]ethylamino]-2-oxidanylidene-ethoxy]ethoxy]ethylamino]-1-oxidanyl-1,5-bis(oxidanylidene)pentan-2-yl]amino]-20-oxidanylidene-icosanoic acid


Mass: 817.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H76N4O12 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Essentially defatted human serum albumin from Sigma was purified by size exclusion chromatography to obtain pure monomeric protein. The purified HSA was dissolved in 20 mM potassium ...Details: Essentially defatted human serum albumin from Sigma was purified by size exclusion chromatography to obtain pure monomeric protein. The purified HSA was dissolved in 20 mM potassium phosphate (pH 7.0) and concentrated to 120 mg/mL. To the HSA solution we added 10 mM cpdX and 3 mM myristate, dissolved DMSO. The final concentration of DMSO was 5% (v/v). The crystal was grown by the hanging drop vapor diffusion method using a reservoir solution containing 50 mM sodium-potassium-phosphate (pH 7.0), and 30% polyethylene glycol 3350. For crystallization 1 uL of HSA/cpdX solution was equilibrated against 1 uL of reservoir solution. After about one-week, colorless crystals appeared.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Aug 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→58.51 Å / Num. obs: 53533 / % possible obs: 96.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 31.56 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.043 / Rrim(I) all: 0.077 / Net I/σ(I): 11.7 / Num. measured all: 156458 / Scaling rejects: 12
Reflection shellResolution: 1.89→1.897 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.1 / Num. measured all: 20574 / Num. unique obs: 7654 / CC1/2: 0.735 / Rpim(I) all: 0.344 / Rrim(I) all: 0.62 / Net I/σ(I) obs: 2.3 / % possible all: 91.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
BUSTERrefinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house structure

Resolution: 1.89→58.51 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.829 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.203 / SU Rfree Blow DPI: 0.197 / SU Rfree Cruickshank DPI: 0.188
RfactorNum. reflection% reflectionSelection details
Rfree0.313 2690 5.03 %RANDOM
Rwork0.239 ---
obs0.243 53531 96.2 %-
Displacement parametersBiso max: 112.86 Å2 / Biso mean: 36.59 Å2 / Biso min: 6.89 Å2
Baniso -1Baniso -2Baniso -3
1--4.477 Å20 Å2-4.0171 Å2
2--0.6185 Å20 Å2
3---3.8586 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 1.89→58.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4479 0 144 662 5285
Biso mean--42.23 39.71 -
Num. residues----568
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1753SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes127HARMONIC2
X-RAY DIFFRACTIONt_gen_planes667HARMONIC5
X-RAY DIFFRACTIONt_it4735HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion594SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6502SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4735HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6360HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion21.99
LS refinement shellResolution: 1.89→1.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 215 5.6 %
Rwork0.245 3621 -
all0.25 3836 -
obs--94.25 %

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