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- PDB-5yoq: Human serum albumin complexed with sodium 4-phenylbutyrate -

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Basic information

Entry
Database: PDB / ID: 5yoq
TitleHuman serum albumin complexed with sodium 4-phenylbutyrate
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / 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; 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
4-PHENYL-BUTANOIC ACID / PHOSPHATE ION / Albumin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKawai, A. / Otagiri, M.
CitationJournal: Biochem Biophys Rep / Year: 2018
Title: Crystal structure analysis of human serum albumin complexed with sodium 4-phenylbutyrate.
Authors: Kawai, A. / Yamasaki, K. / Enokida, T. / Miyamoto, S. / Otagiri, M.
History
DepositionOct 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,6616
Polymers133,1422
Non-polymers5184
Water0
1
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8303
Polymers66,5711
Non-polymers2592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-10 kcal/mol
Surface area26860 Å2
MethodPISA
2
B: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8303
Polymers66,5711
Non-polymers2592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-7 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.465, 181.913, 59.474
Angle α, β, γ (deg.)90.00, 105.16, 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.: 2
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: Pichia (fungus) / References: UniProt: P02768
#2: Chemical ChemComp-CLT / 4-PHENYL-BUTANOIC ACID / GAMMA-PHENYL-BUTYRIC ACID


Mass: 164.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28%(w/v) PEG 3350, 10%(v/v) MPD, 50mM potassium phosphate buffer pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 34871 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 35.7
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.83 / Num. unique obs: 1751 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X52

5x52


Resolution: 2.65→45.348 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.1
RfactorNum. reflection% reflection
Rfree0.2555 1787 5.15 %
Rwork0.2351 --
obs0.2361 34671 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.65→45.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8407 0 34 0 8441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028637
X-RAY DIFFRACTIONf_angle_d0.41511782
X-RAY DIFFRACTIONf_dihedral_angle_d8.025334
X-RAY DIFFRACTIONf_chiral_restr0.0341363
X-RAY DIFFRACTIONf_plane_restr0.0031541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.72170.2831470.28332490X-RAY DIFFRACTION100
2.7217-2.80180.31811560.28522506X-RAY DIFFRACTION100
2.8018-2.89220.36391490.3062515X-RAY DIFFRACTION100
2.8922-2.99550.37271340.30412533X-RAY DIFFRACTION100
2.9955-3.11540.36021040.32573X-RAY DIFFRACTION100
3.1154-3.25720.31651330.2852534X-RAY DIFFRACTION100
3.2572-3.42890.30451410.27082524X-RAY DIFFRACTION100
3.4289-3.64360.26661130.25932548X-RAY DIFFRACTION100
3.6436-3.92480.22921220.23422555X-RAY DIFFRACTION100
3.9248-4.31950.25391500.212497X-RAY DIFFRACTION100
4.3195-4.94380.23371460.20552545X-RAY DIFFRACTION100
4.9438-6.22620.29461450.2512517X-RAY DIFFRACTION100
6.2262-45.35420.1871470.18782547X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.94580.08191.27644.1282-1.3465.7550.2126-0.1716-0.61760.7118-0.01620.68261.4393-0.3844-0.21291.1596-0.09650.22660.5476-0.03670.559410.0321-11.917334.7821
21.9021-0.19590.19912.44730.58171.4581-0.3170.00190.00220.26510.1360.45630.2671-0.06850.180.7532-0.02260.11840.4474-0.01020.356517.38264.099224.7994
32.23790.10390.02563.52610.37021.0003-0.24230.24260.0718-0.59420.3028-0.5449-0.19230.2905-0.01290.818-0.14870.12340.4903-0.09870.377433.27510.33659.9929
43.1792-1.17-0.16271.1178-0.86661.9220.15520.39010.0477-0.8495-0.11350.29430.1541-0.27660.01511.0271-0.1135-0.2020.5239-0.09130.46017.50627.47250.5314
53.7759-2.83593.86144.0109-1.67437.2282-0.3119-0.0441.1830.15050.32140.9661-0.7793-1.1254-0.01850.47090.00570.05310.75660.33791.285-5.304957.728113.1797
64.8417-3.97392.11183.8654-0.42745.9868-0.26130.35482.0894-0.55460.4386-0.6319-0.83430.373-0.41520.9164-0.05940.02370.64110.32061.98570.701969.069916.5403
70.94180.0254-0.83146.88230.34462.73270.06530.01720.10780.63010.24350.44730.2680.1242-0.32430.34030.0318-0.00720.48050.10580.91091.86841.716919.3349
82.40170.7711-0.45182.0603-0.59851.2329-0.13471.01020.7343-0.30540.45260.62350.0214-0.0862-0.28990.4115-0.0669-0.08390.82730.32350.857212.941450.65983.4416
92.49992.257-1.07432.3157-0.58522.0564-0.28141.00210.1803-0.15610.5240.16070.04510.6435-0.1720.7317-0.0603-0.12391.34770.11510.634722.336649.0174-9.8062
102.25210.4867-1.22181.8098-0.28274.45350.19770.81640.3175-0.37730.1609-0.3185-0.05120.2001-0.25870.44920.05590.10150.7769-0.05490.880637.483949.08675.0913
113.43531.608-0.41785.9275-0.89872.9420.2495-0.16770.35460.6493-0.0524-0.1328-0.04760.3288-0.16130.3810.0433-0.08120.4723-0.07840.687728.895845.982623.4023
121.24941.4341.4785.57212.83462.0770.316-0.7075-0.46252.7215-0.294-1.59330.0610.01340.06821.25960.0779-0.36140.66220.251.206230.080430.914439.5162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 104 )
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 249 )
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 437 )
4X-RAY DIFFRACTION4chain 'A' and (resid 438 through 573 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 55 )
6X-RAY DIFFRACTION6chain 'B' and (resid 56 through 105 )
7X-RAY DIFFRACTION7chain 'B' and (resid 106 through 173 )
8X-RAY DIFFRACTION8chain 'B' and (resid 174 through 266 )
9X-RAY DIFFRACTION9chain 'B' and (resid 267 through 342 )
10X-RAY DIFFRACTION10chain 'B' and (resid 343 through 414 )
11X-RAY DIFFRACTION11chain 'B' and (resid 415 through 535 )
12X-RAY DIFFRACTION12chain 'B' and (resid 536 through 569 )

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