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Yorodumi- PDB-6ci6: Crystal structure of equine serum albumin in complex with nabumetone -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ci6 | ||||||
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Title | Crystal structure of equine serum albumin in complex with nabumetone | ||||||
Components | Serum albumin | ||||||
Keywords | TRANSPORT 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 / 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 | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Venkataramany, 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
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ci6.cif.gz | 133.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ci6.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ci6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/6ci6 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/6ci6 | HTTPS FTP |
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-Related structure data
Related structure data | 5v0vC 6u4rC 6u4xC 6u5aC 3v08S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | 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 / #3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Chemical | ChemComp-KNA / | #6: Chemical | ChemComp-UNX / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.98 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97949 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.17 Å2 / Biso mean: 64.159 Å2 / Biso min: 26.05 Å2
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Refinement step | Cycle: final / Resolution: 2.8→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.801→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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