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- PDB-7y2d: HSA-Cu agent complex -

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Basic information

Entry
Database: PDB / ID: 7y2d
TitleHSA-Cu agent complex
ComponentsSerum albumin
KeywordsMETAL BINDING PROTEIN / Complex
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 / small molecule 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-IC4 / PALMITIC ACID / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, Z.L. / Yang, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077021 China
CitationJournal: To Be Published
Title: Structure of HSA-Cu agent complex
Authors: Zhang, Z.L. / Yang, F.
History
DepositionJun 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3839
Polymers66,2151
Non-polymers2,1688
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.330, 38.830, 95.000
Angle α, β, γ (deg.)90.000, 105.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Serum albumin /


Mass: 66214.844 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: Escherichia coli (E. coli) / References: UniProt: P02768
#2: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IC4 / 13-methoxy-~{N},~{N}-dimethyl-2-oxa-4-thia-6,7$l^{4}-diaza-3$l^{3}-cupratricyclo[7.4.0.0^{3,7}]trideca-1(9),5,7,10,12-pentaen-5-amine


Mass: 314.851 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13CuN3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, MPD, DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 16, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→46.09 Å / Num. obs: 44865 / % possible obs: 99.68 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.7
Reflection shellResolution: 2→2.18 Å / Rmerge(I) obs: 0.061 / Num. unique obs: 9780

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YB1

5yb1


Resolution: 2→30.062 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 40.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2861 2186 4.87 %
Rwork0.2328 42660 -
obs0.2354 44846 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.82 Å2 / Biso mean: 62.4389 Å2 / Biso min: 34.48 Å2
Refinement stepCycle: final / Resolution: 2→30.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4443 0 137 82 4662
Biso mean--66.86 60.71 -
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014684
X-RAY DIFFRACTIONf_angle_d1.1016335
X-RAY DIFFRACTIONf_chiral_restr0.054705
X-RAY DIFFRACTIONf_plane_restr0.006816
X-RAY DIFFRACTIONf_dihedral_angle_d16.582927
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.04350.52081580.4776262999
2.0435-2.0910.47681260.45392609100
2.091-2.14330.42951110.41582699100
2.1433-2.20120.43341250.3892262299
2.2012-2.2660.43231370.35962661100
2.266-2.33910.4021210.3452632100
2.3391-2.42260.35241330.31732691100
2.4226-2.51960.39091500.30662611100
2.5196-2.63420.34261390.29052682100
2.6342-2.7730.37111340.30332685100
2.773-2.94660.42051490.30782623100
2.9466-3.17390.31021480.28492651100
3.1739-3.49280.31131420.2574266699
3.4928-3.99730.25851270.2045268799
3.9973-5.03230.23221290.173271799
5.0323-8.0620.21811570.1732795100

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