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- PDB-7dl4: Crystal structure of human serum albumin and nitrosylruthenium co... -

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Basic information

Entry
Database: PDB / ID: 7dl4
TitleCrystal structure of human serum albumin and nitrosylruthenium complex adduct
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Ruthenium complexes / NO donors / Photodynamic / human serum albumin
Function / homology
Function and homology information


exogenous protein binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / 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 / 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
5-chloranylquinolin-8-ol / NITRIC OXIDE / PALMITIC ACID / RUTHENIUM ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXie, L.L. / Wang, W.M. / Wang, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)21671125, 62075118 China
CitationJournal: To Be Published
Title: Structural and Photodynamic Studies on Nitrosylruthenium Complexed Serum Albumin
Authors: Xie, L.L. / Wang, W.M. / Wang, H.F.
History
DepositionNov 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)68,99023
Polymers66,5711
Non-polymers2,41922
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-19 kcal/mol
Surface area29890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.983, 38.494, 95.516
Angle α, β, γ (deg.)90.000, 105.530, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#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: Homo sapiens (human) / References: UniProt: P02768

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Non-polymers , 8 types, 136 molecules

#2: Chemical ChemComp-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ru / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HZQ / 5-chloranylquinolin-8-ol


Mass: 179.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6ClNO
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H32O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 32% PEG3350, 50 mM pottasium phosphate buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25509 / % possible obs: 98.4 % / Redundancy: 4 % / Biso Wilson estimate: 56.7 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.058 / Rrim(I) all: 0.117 / Χ2: 1.089 / Net I/σ(I): 5 / Num. measured all: 101803
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.30.71912130.8980.4510.8540.44597.4
2.44-2.493.30.72512090.8540.4470.8570.47396.1
2.49-2.533.70.6512620.9010.3860.760.46197.6
2.53-2.594.10.58412930.9140.330.6740.48399.5
2.59-2.644.20.50412520.9490.2810.5790.49899.4
2.64-2.74.10.44612850.9540.2520.5140.50699.6
2.7-2.774.20.39312900.9560.2180.4520.53999.8
2.77-2.854.20.3212500.9690.1810.3690.57499.4
2.85-2.934.20.28813090.9760.1610.3310.62499.5
2.93-3.024.10.24312680.9810.1370.280.64498.8
3.02-3.1340.212670.9770.1160.2320.70499.1
3.13-3.263.70.1712360.9870.1010.1990.88495
3.26-3.414.30.14612820.9860.0810.1671.12298.9
3.41-3.584.30.12612690.9860.070.1441.3899.1
3.58-3.814.30.11213060.9870.0630.1291.78799.3
3.81-4.14.10.09312830.9920.0530.1072.0198.9
4.1-4.5240.07812900.9930.0460.0912.15798.5
4.52-5.173.80.07212790.9920.0430.0842.20997
5.17-6.514.20.06513300.9950.0370.0751.6499.3
6.51-503.70.06113360.9920.0360.0722.29996

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Processing

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

5giy


Resolution: 2.4→35.539 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 1235 4.84 %
Rwork0.2081 24265 -
obs0.211 25500 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.81 Å2 / Biso mean: 64.6739 Å2 / Biso min: 32.87 Å2
Refinement stepCycle: final / Resolution: 2.4→35.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 143 114 4876
Biso mean--65.8 63.58 -
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094861
X-RAY DIFFRACTIONf_angle_d0.9556512
X-RAY DIFFRACTIONf_chiral_restr0.047707
X-RAY DIFFRACTIONf_plane_restr0.005833
X-RAY DIFFRACTIONf_dihedral_angle_d20.0393056
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.49610.37481330.3229255395
2.4961-2.60970.32571240.2969269599
2.6097-2.74720.33491460.26282719100
2.7472-2.91930.32231380.2553268999
2.9193-3.14450.31871260.2538270899
3.1445-3.46080.35181420.2349264997
3.4608-3.9610.25081440.1996272699
3.961-4.98820.22391500.175270298
4.9882-35.5390.23441320.1777282498

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