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- PDB-6ci6: Crystal structure of equine serum albumin in complex with nabumetone -

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Basic information

Entry
Database: PDB / ID: 6ci6
TitleCrystal structure of equine serum albumin in complex with nabumetone
ComponentsSerum albumin
KeywordsTRANSPORT PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / serum albumin / equine / nabumetone
Function / homology
Function and homology information


cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / fatty acid binding / cellular response to starvation / pyridoxal phosphate binding / protein-containing complex / extracellular space / DNA binding ...cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / fatty acid binding / cellular response to starvation / pyridoxal phosphate binding / protein-containing complex / extracellular space / DNA binding / 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
nonanoic acid / nabumetone / Albumin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVenkataramany, B.S. / Czub, M.P. / Shabalin, I.G. / Handing, K.B. / Steen, E.H. / Cooper, D.R. / Joachimiak, A. / Satchell, K.J.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 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 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 13, 2020Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Jul 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
Revision 1.4Oct 4, 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)67,07118
Polymers65,8541
Non-polymers1,21717
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-63 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.879, 93.879, 140.787
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: 65854.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P35747

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Non-polymers , 6 types, 113 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NBO / nabumetone / 4-(6-methoxynaphthalen-2-yl)butan-2-one


Mass: 228.286 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-KNA / nonanoic acid


Mass: 158.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H18O2
#6: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 54.98 %
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 7.4 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl, 2.2 M (NH4)2SO4 final pH 7.4) and equilibrated ...Details: 1 ul of 34 mg/ml protein in 10 mM Tris pH 7.4 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl, 2.2 M (NH4)2SO4 final pH 7.4) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). Crystals were soaked with 10 mM nabumetone

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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: 2.8→50.01 Å / Num. obs: 17321 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 63.9 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.057 / Rrim(I) all: 0.129 / Rsym value: 0.115 / Χ2: 0.73 / Net I/av σ(I): 14.1 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
2.8-2.854.90.668710.8160.3350.7420.660.464100
2.85-2.94.80.5778640.8510.2930.6480.471100
2.9-2.965.20.4978520.8840.2440.5540.487100
2.96-3.025.20.3928640.9240.1930.4380.496100
3.02-3.085.20.3668450.9350.1780.4070.507100
3.08-3.155.10.318770.9420.1520.3460.57100
3.15-3.235.10.2728650.9560.1340.3040.534100
3.23-3.324.80.2158550.9690.1090.2420.56599.8
3.32-3.4250.188500.9770.0890.2010.589100
3.42-3.535.10.1588690.980.0780.1770.58299.9
3.53-3.6550.1388700.9860.0690.1550.646100
3.65-3.85.30.1268600.9850.0610.140.71899.9
3.8-3.975.30.1088660.9890.0520.120.735100
3.97-4.185.20.0958610.990.0470.1060.76100
4.18-4.4450.098740.9920.0450.1010.86799.8
4.44-4.7950.0858650.9930.0420.0950.901100
4.79-5.275.30.0878680.9920.0410.0960.919100
5.27-6.035.20.0878710.9920.0420.0970.89100
6.03-7.594.90.0778700.9940.0380.0861.03699.9
7.59-5050.0659040.9950.0320.0731.79699.9

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-3000data reduction
MOLREPphasing
HKL-3000phasing
PDB_EXTRACT3.22data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V08

3v08


Resolution: 2.8→50.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.905 / SU B: 17.5 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 788 4.6 %RANDOM
Rwork0.1824 ---
obs0.1858 16496 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.17 Å2 / Biso mean: 64.159 Å2 / Biso min: 26.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20.84 Å20 Å2
2--1.69 Å2-0 Å2
3----5.47 Å2
Refinement stepCycle: final / Resolution: 2.8→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4524 0 86 96 4706
Biso mean--75.82 48.4 -
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194710
X-RAY DIFFRACTIONr_bond_other_d0.0060.024311
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.986379
X-RAY DIFFRACTIONr_angle_other_deg0.861310058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8375580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82624.854206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86915810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.271520
X-RAY DIFFRACTIONr_chiral_restr0.0550.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215318
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02902
LS refinement shellResolution: 2.801→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 60 -
Rwork0.294 1163 -
all-1223 -
obs--97.14 %

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