+Open data
-Basic information
Entry | Database: PDB / ID: 1bm0 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN SERUM ALBUMIN | ||||||
Components | SERUM ALBUMIN | ||||||
Keywords | CARRIER PROTEIN / ALBUMIN | ||||||
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 / small molecule 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sugio, S. / Kashima, A. / Mochizuki, S. / Noda, M. / Kobayashi, K. | ||||||
Citation | Journal: Protein Eng. / Year: 1999 Title: Crystal structure of human serum albumin at 2.5 A resolution. Authors: Sugio, S. / Kashima, A. / Mochizuki, S. / Noda, M. / Kobayashi, K. #1: Journal: Adv.Protein Chem. / Year: 1994 Title: Structure of Serum Albumin Authors: Carter, D.C. / Ho, J.X. #2: Journal: Eur.J.Biochem. / Year: 1994 Title: Preliminary Crystallographic Studies of Four Crystal Forms of Serum Albumin Authors: Carter, D.C. / Chang, B. / Ho, J.X. / Keeling, K. / Krishnasami, Z. #3: Journal: Nature / Year: 1993 Title: Erratum. Atomic Structure and Chemistry of Human Serum Albumin Authors: He, X.M. / Carter, D.C. #4: Journal: Nature / Year: 1992 Title: Atomic Structure and Chemistry of Human Serum Albumin Authors: He, X.M. / Carter, D.C. #5: Journal: Science / Year: 1990 Title: Structure of Human Serum Albumin Authors: Carter, D.C. / He, X.M. #6: Journal: Science / Year: 1989 Title: Three-Dimensional Structure of Human Serum Albumin Authors: Carter, D.C. / He, X.M. / Munson, S.H. / Twigg, P.D. / Gernert, K.M. / Broom, M.B. / Miller, T.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bm0.cif.gz | 225.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bm0.ent.gz | 187.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bm0_validation.pdf.gz | 377.2 KB | Display | wwPDB validaton report |
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Full document | 1bm0_full_validation.pdf.gz | 405.2 KB | Display | |
Data in XML | 1bm0_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 1bm0_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/1bm0 ftp://data.pdbj.org/pub/pdb/validation_reports/bm/1bm0 | HTTPS FTP |
-Related structure data
Related structure data | 1ao6SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 66571.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: PLASMA / Production host: Pichia pastoris (fungus) / References: UniProt: P02768 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.76 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 77 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop / PH range low: 5.5 / PH range high: 5 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 14, 1996 / Details: YALE/MSC MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→93.47 Å / Num. obs: 36149 / % possible obs: 71.3 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 4.37 |
Reflection shell | Resolution: 2.37→2.5 Å / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 1.52 / % possible all: 36.1 |
Reflection shell | *PLUS % possible obs: 36 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HUMAN SERUM ALBUMIN (1AO6) Resolution: 2.5→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: POSTERIORI / σ(F): 0 Details: THE AUTHORS USED BULK SOLVENT CORRECTION AND WEIGHTING SCHEME DEPENDENT ON RESOLUTIONS.
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Displacement parameters | Biso mean: 40.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.42 / Rfactor obs: 0.292 |