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- PDB-9eos: Human serum albumin with myristate -

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Basic information

Entry
Database: PDB / ID: 9eos
TitleHuman serum albumin with myristate
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / serum 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 / endoplasmic reticulum lumen / copper ion binding / 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 / TRIETHYLENE GLYCOL / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFreitag-Pohl, S. / Pohl, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2020-218 United Kingdom
CitationJournal: To Be Published
Title: Human serum albumin with myristate
Authors: Freitag-Pohl, S. / Pohl, E.
History
DepositionMar 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Albumin
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,88010
Polymers139,1662
Non-polymers1,7158
Water3,855214
1
A: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4185
Polymers69,5831
Non-polymers8354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4625
Polymers69,5831
Non-polymers8794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.321, 87.113, 97.471
Angle α, β, γ (deg.)74.443, 89.779, 78.573
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 3 - 583 / Label seq-ID: 27 - 607

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Albumin


Mass: 69582.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: synthetic HSA GenBank AAX36126.1 / Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Escherichia coli (E. coli) / 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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.22 Å3/Da / Density % sol: 44.53 % / Description: rods, seeding is needed, otherwise hollow rods
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 mM Potassium phosphate pH 7.5, 31-34 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→72.34 Å / Num. obs: 67849 / % possible obs: 97.8 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.036 / Rrim(I) all: 0.07 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
9.85-72.343.80.0321.96620.9950.0190.03699.1
2.1-2.153.20.4162.642550.8470.2750.50190.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→72.34 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.088 / SU ML: 0.182 / Cross valid method: FREE R-VALUE / ESU R: 0.26 / ESU R Free: 0.218
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2689 3261 4.808 %
Rwork0.2111 64569 -
all0.214 --
obs-67830 97.696 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 45.402 Å2
Baniso -1Baniso -2Baniso -3
1--0.475 Å2-0.491 Å20.553 Å2
2--2.238 Å2-1.029 Å2
3----2.428 Å2
Refinement stepCycle: LAST / Resolution: 2.1→72.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8813 0 119 214 9146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0129147
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168453
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.65412402
X-RAY DIFFRACTIONr_angle_other_deg0.4691.57119479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98851168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.989542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.955101453
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.22710385
X-RAY DIFFRACTIONr_chiral_restr0.0710.21410
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021979
X-RAY DIFFRACTIONr_nbd_refined0.2190.22205
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.27187
X-RAY DIFFRACTIONr_nbtor_refined0.1820.24552
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.25034
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0640.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2880.211
X-RAY DIFFRACTIONr_nbd_other0.2020.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.211
X-RAY DIFFRACTIONr_mcbond_it4.2724.7114666
X-RAY DIFFRACTIONr_mcbond_other4.2724.7114666
X-RAY DIFFRACTIONr_mcangle_it5.6138.465830
X-RAY DIFFRACTIONr_mcangle_other5.6138.465831
X-RAY DIFFRACTIONr_scbond_it5.1785.1844481
X-RAY DIFFRACTIONr_scbond_other5.1785.1844482
X-RAY DIFFRACTIONr_scangle_it7.5069.3436570
X-RAY DIFFRACTIONr_scangle_other7.5069.3446571
X-RAY DIFFRACTIONr_lrange_it8.74646.08110245
X-RAY DIFFRACTIONr_lrange_other8.74846.09110222
X-RAY DIFFRACTIONr_ncsr_local_group_10.0840.0517573
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.083790.05008
12AX-RAY DIFFRACTIONLocal ncs0.083790.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1540.352210.2954435X-RAY DIFFRACTION90.7956
2.154-2.2130.3392240.2714623X-RAY DIFFRACTION96.5538
2.213-2.2780.3212540.2614486X-RAY DIFFRACTION97.4106
2.278-2.3480.3152000.2274382X-RAY DIFFRACTION97.5309
2.348-2.4240.2772100.2124319X-RAY DIFFRACTION97.6709
2.424-2.5090.2622070.2074094X-RAY DIFFRACTION98.0173
2.509-2.6040.3272350.2333946X-RAY DIFFRACTION97.9845
2.604-2.710.3432060.2473849X-RAY DIFFRACTION98.2078
2.71-2.8310.2931790.2393695X-RAY DIFFRACTION98.4248
2.831-2.9680.3391870.2493550X-RAY DIFFRACTION98.4976
2.968-3.1290.2411590.2333360X-RAY DIFFRACTION98.6267
3.129-3.3180.2781450.2343186X-RAY DIFFRACTION98.8427
3.318-3.5470.2561450.213024X-RAY DIFFRACTION98.9385
3.547-3.830.2621350.1952837X-RAY DIFFRACTION99.0007
3.83-4.1950.2321190.1792573X-RAY DIFFRACTION99.1529
4.195-4.6880.2091140.162316X-RAY DIFFRACTION99.1837
4.688-5.4090.241290.182053X-RAY DIFFRACTION99.3625
5.409-6.6160.325820.2271738X-RAY DIFFRACTION99.4536
6.616-9.3170.195640.1651363X-RAY DIFFRACTION99.86
9.317-72.340.231460.208740X-RAY DIFFRACTION99.6198

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