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Yorodumi- PDB-7mbl: Crystal structure of Equine Serum Albumin in complex with Cobalt (II) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mbl | ||||||
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Title | Crystal structure of Equine Serum Albumin in complex with Cobalt (II) | ||||||
Components | Serum albumin | ||||||
Keywords | TRANSPORT PROTEIN / serum albumin / complex with Cobalt / Structural Genomics / Center for Structural Genomics of Infectious Diseases / 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 | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Shabalin, I.G. / Czub, M.P. / Handing, K.B. / Cymborowski, M.T. / Grabowski, M. / Cooper, D.R. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Equine Serum Albumin in complex with Cobalt Authors: Shabalin, I.G. / Czub, M.P. / Handing, K.B. / Grabowski, M. / Cooper, D.R. / Minor, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mbl.cif.gz | 244.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mbl.ent.gz | 197.9 KB | Display | PDB format |
PDBx/mmJSON format | 7mbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/7mbl ftp://data.pdbj.org/pub/pdb/validation_reports/mb/7mbl | HTTPS FTP |
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-Related structure data
Related structure data | 5iiuS S: Starting model for refinement |
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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 / Source method: isolated from a natural source Details: isolated from blood of common horse (Equus caballus) Source: (natural) Equus caballus (horse) / Tissue: blood / References: UniProt: P35747 | ||||||
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#2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.51 % |
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Crystal grow | Temperature: 291 K / Method: counter-diffusion / pH: 7.4 Details: Protein: 1 uL of 34 mg/mL ESA dissolved in 10 mM Tris (pH 7.4) and 150 mM NaCl. Precipitant: 1 uL of 0.2 M lithium sulfate, 2.0 M ammonium sulfate, 0.1 M Tris pH 7.4. 15-Well hanging drop ...Details: Protein: 1 uL of 34 mg/mL ESA dissolved in 10 mM Tris (pH 7.4) and 150 mM NaCl. Precipitant: 1 uL of 0.2 M lithium sulfate, 2.0 M ammonium sulfate, 0.1 M Tris pH 7.4. 15-Well hanging drop crystallization plate (Qiagen, EasyXtal). 3.3 uL of 50 mM cobalt (II) chloride dissolved in the reservoir solution were added directly to the 2 uL crystallization drop containing crystals to reach a final cobalt concentration of 31 mM and then incubated for a few hours before harvesting. Paratone was used as a cryoprotectant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97929 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) Rosenbaum-Rock double-crystal monochromator: water cooled; Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 19239 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 54.2 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.044 / Rrim(I) all: 0.099 / Rsym value: 0.089 / Χ2: 0.854 / Net I/av σ(I): 17.28 / Net I/σ(I): 7.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IIU Resolution: 2.7→46.7 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.877 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.1802 / FOM work R set: 0.7456 / SU B: 35.506 / SU ML: 0.335 / SU Rfree: 0.4264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 177.97 Å2 / Biso mean: 58.041 Å2 / Biso min: 16.03 Å2
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Refinement step | Cycle: final / Resolution: 2.7→46.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 40.105 Å / Origin y: 16.756 Å / Origin z: 70.759 Å
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