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Yorodumi- PDB-5ij5: Crystal structure of Equine Serum Albumin in the presence of 50 m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ij5 | ||||||||||||
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Title | Crystal structure of Equine Serum Albumin in the presence of 50 mM zinc at pH 4.5 | ||||||||||||
Components | Serum albumin | ||||||||||||
Keywords | TRANSPORT PROTEIN / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC | ||||||||||||
Function / homology | Function and homology information cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / small molecule binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / blood microparticle / protein-containing complex ...cellular response to calcium ion starvation / enterobactin binding / negative regulation of mitochondrial depolarization / toxic substance binding / small molecule binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / blood microparticle / protein-containing complex / DNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Equus caballus (horse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||||||||
Authors | Handing, K.B. / Majorek, K.A. / Shabalin, I.G. / Cymborowski, M.T. / Zheng, H. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Chem Sci / Year: 2016 Title: Circulatory zinc transport is controlled by distinct interdomain sites on mammalian albumins. Authors: Handing, K.B. / Shabalin, I.G. / Kassaar, O. / Khazaipoul, S. / Blindauer, C.A. / Stewart, A.J. / Chruszcz, M. / Minor, W. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ij5.cif.gz | 246 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ij5.ent.gz | 197.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ij5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ij5_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 5ij5_full_validation.pdf.gz | 438 KB | Display | |
Data in XML | 5ij5_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 5ij5_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/5ij5 ftp://data.pdbj.org/pub/pdb/validation_reports/ij/5ij5 | HTTPS FTP |
-Related structure data
Related structure data | 5iihSC 5iiuC 5iixC 5ijeC 5ijfC 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
#1: Protein | Mass: 65768.086 Da / Num. of mol.: 1 / Fragment: residues 25-607 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P35747 | ||||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Sequence details | In contrast with the previously deposited in PDB structures of Equus caballus SA (PDB IDs: 3V08, ...In contrast with the previously deposited in PDB structures of Equus caballus SA (PDB IDs: 3V08, 4J2V, 4OT2, 4F5U, and 4F5T), a single point mutation, R561A, is observed. The long arginine side chain cannot be modeled in this position due to steric clashes with the nearby disulfide bond connecting Cys567 and Cys558 and a symmetry-related copy of the molecule. Moreover, there is no 2mFo-DFc omit map supporting placement of the side chain. Protein was purified from natural source, therefore there may be naturally occurring mutation. According to the NCBI database, this mutation is characteristic for Equus ferus przewalskii, a rare subspecies of wild horse from central Asia (accession code: XP_008524663.1). However it is possible that there is an error in the Equus caballus SA sequence, or the observed mutation naturally occurs in that species. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.93 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 1 ul of 30 mg/ml protein in 10 mM Tris pH 7.5 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (2.0 M (NH4)2SO4, 0.1 M Na acetate, 0.1 M ZnCl2, final pH 4.5) and equilibrated ...Details: 1 ul of 30 mg/ml protein in 10 mM Tris pH 7.5 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (2.0 M (NH4)2SO4, 0.1 M Na acetate, 0.1 M ZnCl2, final pH 4.5) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→50.01 Å / Num. obs: 24491 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/av σ(I): 23.84 / Net I/σ(I): 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IIH Resolution: 2.55→50.01 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 25.457 / SU ML: 0.275 / SU R Cruickshank DPI: 0.4744 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.474 / ESU R Free: 0.292 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 213.27 Å2 / Biso mean: 75.843 Å2 / Biso min: 37.45 Å2
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Refinement step | Cycle: final / Resolution: 2.55→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.555→2.621 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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