+Open data
-Basic information
Entry | Database: PDB / ID: 5otb | ||||||
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Title | Structure of caprine serum albumin in P1 space group | ||||||
Components | Albumin | ||||||
Keywords | TRANSPORT PROTEIN / caprine serum albumin / goat serum albumin / P1 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Capra hircus (goat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Talaj, J.A. / Bujacz, A. / Bujacz, G. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Crystal structures of serum albumins from domesticated ruminants and their complexes with 3,5-diiodosalicylic acid. Authors: Bujacz, A. / Talaj, J.A. / Zielinski, K. / Pietrzyk-Brzezinska, A.J. / Neumann, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5otb.cif.gz | 922.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5otb.ent.gz | 777.4 KB | Display | PDB format |
PDBx/mmJSON format | 5otb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/5otb ftp://data.pdbj.org/pub/pdb/validation_reports/ot/5otb | HTTPS FTP |
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-Related structure data
Related structure data | 5orfC 5oriSC 5oswC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 66412.797 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / Plasmid details: serum plasma / Tissue: Blood / References: UniProt: B3VHM9 #2: Chemical | #3: Chemical | ChemComp-PRO / #4: Chemical | #5: 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: 2.44 Å3/Da / Density % sol: 49.61 % / Description: plate |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0,2M L-Proline, Hepes pH 7,5, 24% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 25, 2013 / Details: mirrors |
Radiation | Monochromator: S 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 85355 / % possible obs: 98.1 % / Redundancy: 3.15 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.97 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.11 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 9218 / CC1/2: 0.596 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ORI Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / SU B: 19.529 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.82 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.673 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→40 Å
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Refine LS restraints |
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