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Yorodumi- PDB-6ocl: Crystal Structure of Leporine Serum Albumin in Complex with Suprofen -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ocl | ||||||
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Title | Crystal Structure of Leporine Serum Albumin in Complex with Suprofen | ||||||
Components | Serum albumin | ||||||
Keywords | TRANSPORT PROTEIN / HELICAL / THREE-DOMAIN PROTEIN / SERUM ALBUMIN | ||||||
Function / homology | Function and homology information cellular response to calcium ion starvation / exogenous protein binding / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / oxygen binding / pyridoxal phosphate binding / protein-folding chaperone binding ...cellular response to calcium ion starvation / exogenous protein binding / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / oxygen binding / pyridoxal phosphate binding / protein-folding chaperone binding / blood microparticle / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular exosome / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Zielinski, K. / Sekula, B. / Bujacz, A. / Bujacz, G. | ||||||
Citation | Journal: Chirality / Year: 2020 Title: Structural investigations of stereoselective profen binding by equine and leporine serum albumins. Authors: Zielinski, K. / Sekula, B. / Bujacz, A. / Szymczak, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ocl.cif.gz | 251.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ocl.ent.gz | 203.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ocl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/6ocl ftp://data.pdbj.org/pub/pdb/validation_reports/oc/6ocl | HTTPS FTP |
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-Related structure data
Related structure data | 6ociC 6ocjC 6ockC 4f5vS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 66173.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Blood / References: UniProt: G1U9S2, UniProt: P49065*PLUS | ||||
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#2: Chemical | ChemComp-M5A / ( | ||||
#3: Chemical | #4: Chemical | ChemComp-PGE / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 8% PPG400, 0.2 M ammonium acetate, 16% PEG 3350, 0.1 M TRIS. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2013 / Details: MIRRORS |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 28848 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.88 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 2.35→2.45 Å / Redundancy: 4.94 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2 / Num. unique obs: 3300 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4F5V Resolution: 2.35→28.67 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 17.636 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 63.793 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→28.67 Å
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