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- PDB-6r7s: Human Serum Albumin, complexed with Sulfasalazine -

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Basic information

Entry
Database: PDB / ID: 6r7s
TitleHuman Serum Albumin, complexed with Sulfasalazine
ComponentsSerum albumin
KeywordsLIPID BINDING PROTEIN / Serum Albumin binding / Fluorescent probe / drug tranport
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsSchreuder, H.A. / Liesum, A.
CitationJournal: Chemmedchem / Year: 2020
Title: Resolving Binding Events on the Multifunctional Human Serum Albumin.
Authors: Wenskowsky, L. / Wagner, M. / Reusch, J. / Schreuder, H. / Matter, H. / Opatz, T. / Petry, S.M.
History
DepositionMar 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)68,0197
Polymers66,5711
Non-polymers1,4486
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-5 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.297, 85.113, 60.123
Angle α, β, γ (deg.)90.00, 99.89, 90.00
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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SAS / 2-HYDROXY-(5-([4-(2-PYRIDINYLAMINO)SULFONYL]PHENYL)AZO)BENZOIC ACID / SULFASALAZINE / Sulfasalazine


Mass: 398.393 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H14N4O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HSA was dissolved in 50 mM potassium phosphate, 150 mM sodium chloride (pH 7.5) and concentrated to 2 mM (140 mg/mL). The HSA solution was incubated with a six fold excess of sulfasalazine ...Details: HSA was dissolved in 50 mM potassium phosphate, 150 mM sodium chloride (pH 7.5) and concentrated to 2 mM (140 mg/mL). The HSA solution was incubated with a six fold excess of sulfasalazine at 4-5 degrees C for 4 hours.The crystal was grown by the hanging drop vapor diffusion method using a reservoir solution containing buffer (2.5 mM potassium phosphate, 7.5 mM sodium chloride, pH 7.0), 0.3% glycerol and polyethylene glycol 3350 (~30%). For crystallization 1 uL protein solution was equilibrated against 1 uL of reservoir solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.208→48.616 Å / Num. obs: 18420 / % possible obs: 62.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 48.12 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 12.7
Reflection shellResolution: 2.208→2.473 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 922 / Rpim(I) all: 0.453 / Rrim(I) all: 0.85 / Rsym value: 0.729 / % possible all: 10.8

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Processing

Software
NameVersionClassification
XDSJun 1, 2017data reduction
STARANISO1.10.17betadata scaling
AutoPROC1.1.7data scaling
Aimlessdata scaling
BUSTER2.11.7refinement
PHASERphasing
AutoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4sly

4sly


Resolution: 2.21→48.616 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.369
RfactorNum. reflection% reflectionSelection details
Rfree0.275 866 4.7 %RANDOM
Rwork0.177 ---
obs0.182 18420 62.1 %-
Displacement parametersBiso mean: 53.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.6903 Å20 Å20.1249 Å2
2--0.8605 Å20 Å2
3----1.5508 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.21→48.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4414 0 97 356 4867
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014640HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.146295HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1604SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes861HARMONIC5
X-RAY DIFFRACTIONt_it4640HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion21.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion593SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5824SEMIHARMONIC4
LS refinement shellResolution: 2.21→2.38 Å / Total num. of bins used: 43
RfactorNum. reflection% reflection
Rfree0.2881 -3.96 %
Rwork0.2249 412 -
all0.2275 429 -
obs--7.24 %

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