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- PDB-5v0v: Crystal structure of Equine Serum Albumin complex with etodolac -

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Basic information

Entry
Database: PDB / ID: 5v0v
TitleCrystal structure of Equine Serum Albumin complex with etodolac
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / Equine Serum Albumin / Etodolac / CSGID
Function / homology
Function and homology information


cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space ...cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space / metal ion binding / 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
Chem-8QP / Chem-8QS / Albumin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsCzub, M.P. / Shabalin, I.G. / Handing, K.B. / Venkataramany, B.S. / Steen, E.H. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM117080 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM118619 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM132595 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Albumin-Based Transport of Nonsteroidal Anti-Inflammatory Drugs in Mammalian Blood Plasma.
Authors: Czub, M.P. / Handing, K.B. / Venkataramany, B.S. / Cooper, D.R. / Shabalin, I.G. / Minor, W.
History
DepositionFeb 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,07916
Polymers65,7681
Non-polymers2,31015
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.209, 94.209, 141.819
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serum albumin /


Mass: 65768.086 Da / Num. of mol.: 1 / Fragment: UNP residues 25-607 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P35747

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Non-polymers , 5 types, 179 molecules

#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-8QP / [(1S)-1,8-diethyl-1,3,4,9-tetrahydropyrano[3,4-b]indol-1-yl]acetic acid / (S)-Etodolac


Mass: 287.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21NO3
#5: Chemical ChemComp-8QS / [(1R)-1,8-diethyl-1,3,4,9-tetrahydropyrano[3,4-b]indol-1-yl]acetic acid / (R)-Etodolac / Etodolac


Mass: 287.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21NO3 / Comment: antiinflammatory*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1 ul of 34 mg/ml protein in 10 mM Tris pH 7.5 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl, 2.0 M (NH4)2SO4 final pH 7.4) and equilibrated ...Details: 1 ul of 34 mg/ml protein in 10 mM Tris pH 7.5 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl, 2.0 M (NH4)2SO4 final pH 7.4) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). Crystals were soaked with 10 mM Etodolac.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2016
Details: 1000 um thick sensor. Mirrors: adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 26311 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 56.7 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.05 / Rrim(I) all: 0.102 / Rsym value: 0.088 / Χ2: 0.68 / Net I/av σ(I): 14 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
2.45-2.493.50.5741.213040.7530.3430.6730.5740.47498.6
2.49-2.543.80.4930.8440.2920.5760.45699.7
2.54-2.5940.5210.830.30.6030.464100
2.59-2.6440.4240.8780.2430.490.469100
2.64-2.740.3790.9070.2170.4380.465100
2.7-2.763.80.3020.9360.1760.3510.473100
2.76-2.834.10.2810.9370.1590.3240.47999.8
2.83-2.93.90.2370.9480.1380.2750.472100
2.9-2.994.10.1880.9690.1060.2170.497100
2.99-3.094.10.1590.9780.0890.1830.541100
3.09-3.240.1320.9820.0750.1530.556100
3.2-3.323.90.1150.9850.0660.1330.617100
3.32-3.4840.0910.9880.0520.1050.68599.9
3.48-3.663.90.0830.990.0480.0960.75599.9
3.66-3.894.10.0790.9910.0440.0910.837100
3.89-4.194.10.070.9910.0390.0810.918100
4.19-4.613.90.0660.9930.0370.0760.996100
4.61-5.284.10.0660.9920.0370.0761.02100
5.28-6.6540.0670.9910.0370.0770.96299.8
6.65-503.90.0570.9930.0320.0651.37599.9

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Processing

Software
NameVersionClassification
HKL-3000data reduction
MOLREPphasing
HKL-3000phasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BQF

5bqf


Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 21.103 / SU ML: 0.235 / SU R Cruickshank DPI: 0.4224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.422 / ESU R Free: 0.262
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1409 5.4 %RANDOM
Rwork0.1801 ---
obs0.1833 24779 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 158.42 Å2 / Biso mean: 64.662 Å2 / Biso min: 33.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20.59 Å20 Å2
2--1.17 Å2-0 Å2
3----3.8 Å2
Refinement stepCycle: final / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4506 0 151 164 4821
Biso mean--85.28 54.83 -
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194774
X-RAY DIFFRACTIONr_bond_other_d0.0060.024322
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9886487
X-RAY DIFFRACTIONr_angle_other_deg0.887310071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9035580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5424.831207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46415794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7571520
X-RAY DIFFRACTIONr_chiral_restr0.0570.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02908
LS refinement shellResolution: 2.45→2.513 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 97 -
Rwork0.326 1815 -
all-1912 -
obs--98.86 %
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)
18.171-1.18973.12773.7936-1.08124.05-0.1874-0.0590.3742-0.18130.07860.0828-0.2609-0.1990.10880.2283-0.03220.05170.2446-0.04170.2548-14.1261.71722.63
22.1661-0.3535-0.3473.3029-0.48722.0974-0.0633-0.61060.18510.34730.1742-0.0926-0.26090.1179-0.11090.3548-0.05470.06070.4923-0.09110.2586-5.17366.90229.658
33.5776-0.7586-0.68861.47320.81241.7882-0.16-0.5138-0.45950.30340.00630.2410.3207-0.17940.15370.2115-0.03150.0190.27360.00040.21923.52950.07724.528
44.2578-0.2359-1.14281.30570.23971.82880.02450.147-0.0718-0.052-0.00860.17080.1577-0.1058-0.0160.2296-0.0189-0.0670.2082-0.04380.09338.39149.5526.46
54.60080.5072-1.58972.0759-0.05045.55820.0270.20490.1262-0.1292-0.0644-0.25-0.18560.28350.03750.15550.0251-0.02020.1835-0.04950.14728.94754.5624.977
61.6494-0.62730.72252.5643-0.75883.5027-0.1119-0.0875-0.01250.00880.04790.02990.01940.0880.06390.16660.01650.03690.2435-0.01360.130624.86155.13330.525
72.77990.1398-1.64010.9859-1.05814.1053-0.0884-0.25640.12850.26420.09850.0433-0.306-0.0675-0.01010.29450.1101-0.0050.2413-0.00240.171127.41353.19653.235
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 60
2X-RAY DIFFRACTION2A61 - 128
3X-RAY DIFFRACTION3A129 - 231
4X-RAY DIFFRACTION4A232 - 320
5X-RAY DIFFRACTION5A321 - 387
6X-RAY DIFFRACTION6A388 - 498
7X-RAY DIFFRACTION7A499 - 583

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