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- PDB-7ffs: Human Serum Albumin_1 -

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Basic information

Entry
Database: PDB / ID: 7ffs
TitleHuman Serum Albumin_1
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Human 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 / 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; 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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsXiang, W. / Yue, Z.L. / Su, J.Y.
CitationJournal: To Be Published
Title: Human Serum Albumin
Authors: Xiang, W. / Yue, Z.L. / Su, J.Y.
History
DepositionJul 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin


Theoretical massNumber of molelcules
Total (without water)66,5711
Polymers66,5711
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.587, 87.123, 58.861
Angle α, β, γ (deg.)90.000, 103.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serum albumin


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.88 %
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: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.05→19.78 Å / Num. obs: 30333 / % possible obs: 88.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 7
Reflection shellResolution: 2.05→2.11 Å / Rmerge(I) obs: 0.511 / Num. unique obs: 2522

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M4R

6m4r


Resolution: 2.05→19.6 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2795 1882 6.55 %
Rwork0.2552 26867 -
obs0.2568 28749 84.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.01 Å2 / Biso mean: 32.018 Å2 / Biso min: 13.91 Å2
Refinement stepCycle: final / Resolution: 2.05→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4521 0 0 226 4747
Biso mean---30.92 -
Num. residues----568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.110.37211540.34292327248195
2.11-2.170.50341630.44422171233490
2.17-2.240.6314560.530691797337
2.24-2.320.6398980.53231187128550
2.32-2.410.33791450.30482255240091
2.41-2.520.28981590.27872248240792
2.52-2.650.28631600.27572233239391
2.65-2.820.29291500.27312201235189
2.82-3.030.31821590.26242246240592
3.03-3.340.27291610.24682261242292
3.34-3.820.2221580.21742278243693
3.82-4.80.21351590.1972282244192
4.8-19.60.21621600.20372261242190

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