+Open data
-Basic information
Entry | Database: PDB / ID: 5ghk | ||||||
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Title | Crystal Structure Analysis of Canine serum albumin | ||||||
Components | Serum albumin | ||||||
Keywords | TRANSPORT PROTEIN / Plasma protein | ||||||
Function / homology | Function and homology information maintenance of mitochondrion location / enterobactin binding / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular space ...maintenance of mitochondrion location / enterobactin binding / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular space / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å | ||||||
Authors | Kihira, K. / Yamada, K. / Kureishi, M. / Yokomaku, K. / Shinohara, R. / Akiyama, M. / Komatsu, T. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Artificial Blood for Dogs Authors: Yamada, K. / Yokomaku, K. / Kureishi, M. / Akiyama, M. / Kihira, K. / Komatsu, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ghk.cif.gz | 121.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ghk.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ghk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/5ghk ftp://data.pdbj.org/pub/pdb/validation_reports/gh/5ghk | HTTPS FTP |
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-Related structure data
Related structure data | 4bkeS S: Starting model for refinement |
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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: 65801.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: ALB / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: F2Z4Q6, UniProt: P49822*PLUS |
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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: 2.23 Å3/Da / Density % sol: 44.75 % / Mosaicity: 1.553 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Morpheus screen condition H1 (Molecular Dimensions) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 23, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 11596 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 49.5 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.046 / Rrim(I) all: 0.12 / Χ2: 2.978 / Net I/av σ(I): 30.259 / Net I/σ(I): 12.3 / Num. measured all: 77559 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BKE Resolution: 3.2→34.836 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0.12 / Phase error: 29.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.65 Å2 / Biso mean: 47.8378 Å2 / Biso min: 18.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→34.836 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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