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- PDB-7ov5: Structure of Human Serum Albumin in complex with Aristolochic Aci... -

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Basic information

Entry
Database: PDB / ID: 7ov5
TitleStructure of Human Serum Albumin in complex with Aristolochic Acid II at 1.9 A resolution
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Human Serum Albumin / Aristolochic Acid II / Complex / High Resolution
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 / 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
Chem-GOR / 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: To Be Published
Title: Structural and mechanistic insights for the binding of aristolochic acids and their active metabolites to human serum albumin
Authors: Pomyalov, S. / Bonala, R. / Johnson, F. / Zaitseva, I. / Iden, C. / Golebievska, U. / Shoham, G. / Sidorenko, V.S.
History
DepositionJun 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)143,17322
Polymers138,9392
Non-polymers4,23420
Water10,701594
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,64912
Polymers69,4701
Non-polymers2,17911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,52410
Polymers69,4701
Non-polymers2,0559
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.821, 38.671, 180.841
Angle α, β, γ (deg.)90.000, 104.926, 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 / Myristic acid


Mass: 228.371 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOR / 6-nitronaphtho[1,2-e][1,3]benzodioxole-5-carboxylic acid


Mass: 311.246 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C16H9NO6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30% PEG3350, 25 mM Sodium Phosphate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97865 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97865 Å / Relative weight: 1
ReflectionResolution: 1.9→174.74 Å / Num. obs: 101166 / % possible obs: 99.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 36.64 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.041 / Rrim(I) all: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 1.217 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4813 / CC1/2: 0.633 / Rpim(I) all: 0.618 / Rrim(I) all: 1.371

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HSC

6hsc


Resolution: 1.9→73.37 Å / SU ML: 0.3382 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.9061
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2746 4715 4.74 %
Rwork0.2353 94662 -
obs0.2372 99377 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→73.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9136 0 300 594 10030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00649648
X-RAY DIFFRACTIONf_angle_d0.762812991
X-RAY DIFFRACTIONf_chiral_restr0.04241418
X-RAY DIFFRACTIONf_plane_restr0.00521773
X-RAY DIFFRACTIONf_dihedral_angle_d23.7983735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.37981450.33153165X-RAY DIFFRACTION98.63
1.92-1.940.39091590.33563131X-RAY DIFFRACTION98.24
1.94-1.970.35571630.32683101X-RAY DIFFRACTION98.19
1.97-1.990.35271640.32733101X-RAY DIFFRACTION98.17
1.99-2.020.37611680.30833116X-RAY DIFFRACTION97.51
2.02-2.050.3461580.29963164X-RAY DIFFRACTION98.63
2.05-2.080.3641690.28833109X-RAY DIFFRACTION99.06
2.08-2.110.34181320.28773217X-RAY DIFFRACTION99.26
2.11-2.140.30151770.27113170X-RAY DIFFRACTION99.38
2.14-2.170.30371600.25863122X-RAY DIFFRACTION98.92
2.17-2.210.31651680.25213132X-RAY DIFFRACTION98.8
2.21-2.250.2921660.25893130X-RAY DIFFRACTION98.36
2.25-2.30.32631570.26193183X-RAY DIFFRACTION98.67
2.3-2.340.31841680.25993079X-RAY DIFFRACTION97.54
2.34-2.390.33041580.25493157X-RAY DIFFRACTION97.56
2.39-2.450.25971550.25333132X-RAY DIFFRACTION97.54
2.45-2.510.28761530.25153072X-RAY DIFFRACTION97.37
2.51-2.580.31081540.2543197X-RAY DIFFRACTION97.7
2.58-2.650.28561570.26313110X-RAY DIFFRACTION98.05
2.65-2.740.30661430.26733159X-RAY DIFFRACTION97.75
2.74-2.840.31861440.26343159X-RAY DIFFRACTION97.81
2.84-2.950.32351520.26963144X-RAY DIFFRACTION97.17
2.95-3.090.31591490.27463126X-RAY DIFFRACTION96.75
3.09-3.250.3121280.25823186X-RAY DIFFRACTION97.41
3.25-3.450.29211530.24883167X-RAY DIFFRACTION98.05
3.45-3.720.27781760.22023181X-RAY DIFFRACTION98.33
3.72-4.090.25741530.20073214X-RAY DIFFRACTION98.22
4.09-4.680.18841600.18423210X-RAY DIFFRACTION97.82
4.69-5.90.23671700.20863213X-RAY DIFFRACTION97.77
5.9-73.370.22851560.19013315X-RAY DIFFRACTION95.02

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