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- PDB-8h0o: Crystal structure of human serum albumin and ruthenium PZA comple... -

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Basic information

Entry
Database: PDB / ID: 8h0o
TitleCrystal structure of human serum albumin and ruthenium PZA complex adduct
ComponentsAlbumin
KeywordsMETAL BINDING PROTEIN / Human serum albumin
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 / 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
NITRIC OXIDE / PALMITIC ACID / PYRAZINE-2-CARBOXAMIDE / RUTHENIUM ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.479 Å
AuthorsGong, W.J. / Wang, Y. / Bai, H.H. / Wang, W.M. / Wang, H.F.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)62075118 China
National Natural Science Foundation of China (NSFC)21671125 China
National Science Foundation (NSF, China)21601112 China
CitationJournal: To Be Published
Title: Crystal structure of human serum albumin and ruthenium PZA complex adduct
Authors: Gong, W.J. / Wang, Y. / Bai, H.H.
History
DepositionSep 30, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 4, 2023Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,43814
Polymers66,5711
Non-polymers1,86713
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-17 kcal/mol
Surface area30140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.441, 38.326, 95.039
Angle α, β, γ (deg.)90.000, 105.100, 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 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: Homo sapiens (human) / References: UniProt: P02768

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Non-polymers , 6 types, 77 molecules

#2: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#4: Chemical ChemComp-PZA / PYRAZINE-2-CARBOXAMIDE / Pyrazinamide


Mass: 123.113 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N3O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#5: Chemical ChemComp-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ru
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: sodium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.479→50 Å / Num. obs: 21103 / % possible obs: 91.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 43.67 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.047 / Rrim(I) all: 0.102 / Χ2: 1.899 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.544.60.3249480.9380.160.3641.03283.4
2.54-2.595.80.3311330.9560.1520.3651.01699.6
2.59-2.645.90.30210980.9640.1380.3331.03899.2
2.64-2.695.80.29611300.9660.1360.3271.12898.9
2.69-2.755.60.25911210.9710.1220.2881.21898
2.75-2.825.50.23810880.9740.1140.2651.29496.7
2.82-2.895.40.22611010.9660.1090.2521.45796.9
2.89-2.965.30.20711240.970.1010.2321.59396.2
2.96-3.055.20.18410750.980.0920.2071.5996
3.05-3.1550.17110730.9820.0860.1931.83794.3
3.15-3.264.60.14210500.9850.0750.1622.13791.9
3.26-3.394.50.12510520.9850.0660.1432.33590.8
3.39-3.554.30.10810040.9890.0590.1242.67787.7
3.55-3.734.10.0989590.9910.0550.1132.81384.5
3.73-3.973.90.0839660.9890.0470.0962.92683.7
3.97-4.273.50.0669240.9940.0390.0783.13678.2
4.27-4.73.50.0599420.9950.0360.073.11182.7
4.7-5.383.70.05710040.9940.0330.0663.0386
5.38-6.784.50.05811220.9940.0310.066394.5
6.78-504.60.04611890.9970.0240.0532.96696.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DL4

7dl4


Resolution: 2.479→36.939 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2942 1993 9.47 %
Rwork0.2396 19052 -
obs0.2448 21045 90.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.51 Å2 / Biso mean: 52.0089 Å2 / Biso min: 25.34 Å2
Refinement stepCycle: final / Resolution: 2.479→36.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4586 0 115 64 4765
Biso mean--54.74 49.09 -
Num. residues----583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114803
X-RAY DIFFRACTIONf_angle_d1.1556456
X-RAY DIFFRACTIONf_chiral_restr0.057706
X-RAY DIFFRACTIONf_plane_restr0.006832
X-RAY DIFFRACTIONf_dihedral_angle_d17.9193017
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4791-2.54110.39471250.288121180
2.5411-2.60980.3671530.2569144399
2.6098-2.68660.37391500.2478144698
2.6866-2.77330.35061530.249145197
2.7733-2.87240.34751490.2691141697
2.8724-2.98730.35521490.2728142096
2.9873-3.12320.36131450.2896138994
3.1232-3.28780.29481420.2666136992
3.2878-3.49360.35171390.2554132889
3.4936-3.76310.3031330.249126285
3.7631-4.14140.26081280.2285122982
4.1414-4.73960.29061270.2251121180
4.7396-5.96730.27731430.2279136090
5.9673-360.20981570.202151795

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