+Open data
-Basic information
Entry | Database: PDB / ID: 1bj5 | ||||||
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Title | HUMAN SERUM ALBUMIN COMPLEXED WITH MYRISTIC ACID | ||||||
Components | HUMAN SERUM ALBUMIN | ||||||
Keywords | PLASMA PROTEIN / METAL-BINDING / LIPID-BINDING | ||||||
Function / homology | Function and homology information cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å | ||||||
Authors | Curry, S. / Mandelkow, H. / Brick, P. / Franks, N. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Crystal structure of human serum albumin complexed with fatty acid reveals an asymmetric distribution of binding sites. Authors: Curry, S. / Mandelkow, H. / Brick, P. / Franks, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bj5.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bj5.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 1bj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bj5_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
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Full document | 1bj5_full_validation.pdf.gz | 448 KB | Display | |
Data in XML | 1bj5_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 1bj5_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/1bj5 ftp://data.pdbj.org/pub/pdb/validation_reports/bj/1bj5 | HTTPS FTP |
-Related 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: 66571.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: SERUM / Gene: ALB / Organ: PLASMA / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02768 |
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#2: Chemical | ChemComp-MYR / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 54 % Description: THESE DATA WERE OBTAINED BY MERGING A 2.76 ANGSTROM DATA SET (97.9% COMPLETE) RECORDED ON HAMBURG BEAMLINE BW7A WITH A 2.5 ANGSTROM DATASET (65.1% COMPLETE) RECORDED ON BEAMLINE 9.5 AT ...Description: THESE DATA WERE OBTAINED BY MERGING A 2.76 ANGSTROM DATA SET (97.9% COMPLETE) RECORDED ON HAMBURG BEAMLINE BW7A WITH A 2.5 ANGSTROM DATASET (65.1% COMPLETE) RECORDED ON BEAMLINE 9.5 AT DARESBURY. THE ABOVE STATISTICS ARE FOR THE MERGED DATA SET. | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion - sitting drop with streak, macroseeding pH: 7.5 Details: CRYSTALS WERE OBTAINED BY VAPOUR DIFFUSION USING THE SITTING DROP TECHNIQUE. EQUAL VOLUMES OF HSA-MYRISTIC ACID COMPLEX (100 MG/ML) WERE MIXED WITH A RESERVOIR SOLUTION CONSISTING OF 25-30% ...Details: CRYSTALS WERE OBTAINED BY VAPOUR DIFFUSION USING THE SITTING DROP TECHNIQUE. EQUAL VOLUMES OF HSA-MYRISTIC ACID COMPLEX (100 MG/ML) WERE MIXED WITH A RESERVOIR SOLUTION CONSISTING OF 25-30% (W/ V) POLYETHYLENE GLYCOL 3350, 50MM POTASSIUM PHOSPHATE PH 7.5. CRYSTALS GREW SPONTANEOUSLY AS CLUSTERS OF RODS. STREAK AND MACROSEEDING WERE USED TO INCREASE CRYSTAL YIELD. CRYSTALS WERE HARVESTED INTO 31% (W/V) PEG 3350, 50MM POTASSIUM PHOSPHATE PH 7.5 CONTAINING 0.1 MM MYRISTIC ACID., vapor diffusion - sitting drop with streak and macroseeding | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.2 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 21836 / % possible obs: 90.7 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 3 / Rsym value: 0.225 / % possible all: 65 |
Reflection shell | *PLUS % possible obs: 65 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION APPLIED
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Displacement parameters | Biso mean: 51.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2792 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.41 |