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- PDB-8rcp: Structure of Human Serum Albumin in complex with Myristic Acid -

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Basic information

Entry
Database: PDB / ID: 8rcp
TitleStructure of Human Serum Albumin in complex with Myristic Acid
ComponentsSerum albumin
KeywordsLIPID BINDING PROTEIN / HSA / Myristic Acid / Albumin
Function / homology
Function and homology information


Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / 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 / platelet alpha granule lumen / cellular response to starvation / 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 / endoplasmic reticulum / Golgi apparatus / 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 / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPomyalov, S. / Sidorenko, V.S. / Grollman, A.P. / Shoham, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural and mechanistic insights into the transport of aristolochic acids and their active metabolites by human serum albumin.
Authors: Pomyalov, S. / Minetti, C.A. / Remeta, D.P. / Bonala, R. / Johnson, F. / Zaitseva, I. / Iden, C. / Golebiewska, U. / Breslauer, K.J. / Shoham, G. / Sidorenko, V.S. / Grollman, A.P.
History
DepositionDec 6, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionJun 26, 2024ID: 7OV1
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,71720
Polymers138,9392
Non-polymers3,77818
Water11,872659
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,35910
Polymers69,4701
Non-polymers1,8899
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,35910
Polymers69,4701
Non-polymers1,8899
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.728, 38.562, 183.557
Angle α, β, γ (deg.)90.000, 104.663, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Serum albumin


Mass: 69469.695 Da / Num. of mol.: 2 / 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.: 16 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 25% PEG3350, 25mM Sodium Phosphate pH 7.0, Streak Seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→88.79 Å / Num. obs: 102879 / % possible obs: 98.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 36.37 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.5
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 4432 / CC1/2: 0.599

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→74.15 Å / SU ML: 0.3518 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4563
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2688 5037 4.91 %
Rwork0.2243 97446 -
obs0.2265 102483 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→74.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9141 0 264 659 10064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00999608
X-RAY DIFFRACTIONf_angle_d0.992412902
X-RAY DIFFRACTIONf_chiral_restr0.04711419
X-RAY DIFFRACTIONf_plane_restr0.00891668
X-RAY DIFFRACTIONf_dihedral_angle_d9.38191454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.49821640.42483040X-RAY DIFFRACTION91.26
1.92-1.940.40641440.38423134X-RAY DIFFRACTION97.33
1.94-1.970.43721420.35463159X-RAY DIFFRACTION98.63
1.97-1.990.36241510.32413271X-RAY DIFFRACTION98.47
1.99-2.020.33762170.28333171X-RAY DIFFRACTION97.86
2.02-2.050.29291590.26983166X-RAY DIFFRACTION98.05
2.05-2.080.30241640.26093200X-RAY DIFFRACTION99.59
2.08-2.110.29991650.26483278X-RAY DIFFRACTION99.51
2.11-2.140.32451790.26513271X-RAY DIFFRACTION98.77
2.14-2.170.30921780.2643157X-RAY DIFFRACTION99.17
2.17-2.210.29531680.25393220X-RAY DIFFRACTION99.38
2.21-2.250.30891760.25113272X-RAY DIFFRACTION99.45
2.25-2.30.2731770.25223209X-RAY DIFFRACTION98.83
2.3-2.340.31871990.24373212X-RAY DIFFRACTION99.59
2.34-2.390.3081630.23813287X-RAY DIFFRACTION98.91
2.39-2.450.31231540.2433245X-RAY DIFFRACTION99.24
2.45-2.510.31461660.24173227X-RAY DIFFRACTION99.36
2.51-2.580.29271870.24993272X-RAY DIFFRACTION98.86
2.58-2.650.31841800.25163185X-RAY DIFFRACTION99.41
2.65-2.740.28611680.24973309X-RAY DIFFRACTION99.6
2.74-2.840.3111750.24563215X-RAY DIFFRACTION99.33
2.84-2.950.34121670.24623319X-RAY DIFFRACTION99.54
2.95-3.090.29711650.24863246X-RAY DIFFRACTION99.45
3.09-3.250.31091410.2343355X-RAY DIFFRACTION99.6
3.25-3.450.29951390.22853291X-RAY DIFFRACTION98.88
3.45-3.720.2381800.19623278X-RAY DIFFRACTION99.57
3.72-4.090.21031670.18393312X-RAY DIFFRACTION99.4
4.09-4.690.18811940.16823322X-RAY DIFFRACTION99.41
4.69-5.90.21391550.18023372X-RAY DIFFRACTION99.38
5.9-74.150.2151530.20373451X-RAY DIFFRACTION96.62

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