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- PDB-6ezq: human Serum Albumin complexed with NBD-C12 fatty acid -

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Basic information

Entry
Database: PDB / ID: 6ezq
Titlehuman Serum Albumin complexed with NBD-C12 fatty acid
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / fatty acid binding site human Serum Albumin NBD Label drug interaction
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; Chain A, Domain 1 - #10 / 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 ...Serum Albumin; Chain A, Domain 1 - #10 / 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 / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.39 Å
AuthorsWenskowsky, L. / Liesum, A. / Schreuder, H.A.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Identification and Characterization of a Single High-Affinity Fatty Acid Binding Site in Human Serum Albumin.
Authors: Wenskowsky, L. / Schreuder, H. / Derdau, V. / Matter, H. / Volkmar, J. / Nazare, M. / Opatz, T. / Petry, S.
History
DepositionNov 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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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)67,3283
Polymers66,5711
Non-polymers7572
Water5,837324
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.480, 52.720, 123.300
Angle α, β, γ (deg.)90.00, 110.10, 90.00
Int Tables number5
Space group name H-MC121

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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) / Tissue: serum / References: UniProt: P02768
#2: Chemical ChemComp-C7K / 12-[(4-nitro-2,1,3-benzoxadiazol-7-yl)amino]dodecanoic acid


Mass: 378.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H26N4O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.57 %
Description: slightly orange crystals in the shape of stacked plates
Crystal growTemperature: 292 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 50 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 50 mM potassium phosphate, 150 mM sodium chloride (pH 7.5) and concentrated to 2 mM (140 mg/mL). The HSA solution was incubated with a six fold excess of the NBD-labelled fatty acid at 4-5 deg.C for 4 hours. The final concentration of dimethyl sulfoxide was 2% (v/v). The crystal was grown by the hanging drop vapor diffusion method using a reservoir solution containing buffer (2.5 mM potassium phosphate, 7.5 mM sodium chloride, pH 7.0), 0.3% glycerol and polyethylene glycol 3350 (~30%). For crystallization 1 uL of HSA-ligand solution was equilibrated against 1 uL of reservoir solution.
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99992 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 2.39→115.79 Å / Num. obs: 13145 / % possible obs: 55.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 60.21 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 8.4
Reflection shellResolution: 2.393→2.725 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.62 / % possible all: 8.5

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Processing

Software
NameVersionClassification
AutoPROCv.1.1.6data collection
XDS(VERSION Jun 1data reduction
XDSjun 1, 2017data reduction
AutoPROC(Version 1.1.7)data scaling
STARANISOdata scaling
BUSTER2.11.7refinement
PHASERphasing
RefinementResolution: 2.39→115.79 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.818 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.529
RfactorNum. reflection% reflectionSelection details
Rfree0.298 611 4.65 %RANDOM
Rwork0.182 ---
obs0.187 13144 55.1 %-
Displacement parametersBiso mean: 50.13 Å2
Baniso -1Baniso -2Baniso -3
1-1.7181 Å20 Å21.1839 Å2
2--0.9986 Å20 Å2
3----2.7167 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.39→115.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4426 0 54 324 4804
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014582HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.266189HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1637SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes123HARMONIC2
X-RAY DIFFRACTIONt_gen_planes650HARMONIC5
X-RAY DIFFRACTIONt_it4582HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion24.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion583SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5673SEMIHARMONIC4
LS refinement shellResolution: 2.39→2.58 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3064 -5.08 %
Rwork0.2435 224 -
all0.2469 236 -
obs--4.84 %

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