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- PDB-9ik6: Human Serum Albumin crystallized with T4, pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 9ik6
TitleHuman Serum Albumin crystallized with T4, pH 6.5
ComponentsAlbumin
KeywordsTRANSPORT PROTEIN / Human Serum Albumin crystallized with T4 / pH 6.5
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 / fatty acid binding / cellular response to starvation / 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 / extracellular space / DNA binding / 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
3,5,3',5'-TETRAIODO-L-THYRONINE / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsXiang, W. / Yue, Z.L. / Su, J.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human Serum Albumin crystallized with T4, pH 6.5
Authors: Xiang, W. / Yue, Z.L. / Su, J.Y.
History
DepositionJun 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9024
Polymers66,5711
Non-polymers2,3313
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-1 kcal/mol
Surface area29770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.965, 88.964, 60.447
Angle α, β, γ (deg.)90.00, 104.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Albumin / HSA


Mass: 66571.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Komagataella pastoris (fungus) / References: UniProt: P02768
#2: Chemical ChemComp-T44 / 3,5,3',5'-TETRAIODO-L-THYRONINE


Mass: 776.870 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H11I4NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.69→19.91 Å / Num. obs: 68111 / % possible obs: 99 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.3
Reflection shellResolution: 1.69→1.72 Å / Rmerge(I) obs: 0.858 / Num. unique obs: 3601

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Processing

SoftwareName: PHENIX / Version: (1.18.2_3874: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→19.91 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 2003 2.94 %
Rwork0.1955 --
obs0.1966 68075 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4565 0 0 447 5012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024747
X-RAY DIFFRACTIONf_angle_d1.7696409
X-RAY DIFFRACTIONf_dihedral_angle_d7.149622
X-RAY DIFFRACTIONf_chiral_restr0.083703
X-RAY DIFFRACTIONf_plane_restr0.011829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.730.30491400.274678X-RAY DIFFRACTION98
1.73-1.780.28351430.26054653X-RAY DIFFRACTION98
1.78-1.830.31271410.25494678X-RAY DIFFRACTION98
1.83-1.890.31321410.23984682X-RAY DIFFRACTION98
1.89-1.960.26681390.23864672X-RAY DIFFRACTION99
1.96-2.040.28641440.22594664X-RAY DIFFRACTION99
2.04-2.130.29631460.21724718X-RAY DIFFRACTION99
2.13-2.240.24591440.21414769X-RAY DIFFRACTION99
2.24-2.380.26951360.20464697X-RAY DIFFRACTION99
2.38-2.560.23481470.19684728X-RAY DIFFRACTION99
2.56-2.820.20471450.19364759X-RAY DIFFRACTION99
2.82-3.230.24151420.20184741X-RAY DIFFRACTION100
3.23-4.060.22731450.17274805X-RAY DIFFRACTION100
4.06-19.910.19881500.17564828X-RAY DIFFRACTION99

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