+Open data
-Basic information
Entry | Database: PDB / ID: 1n5u | ||||||
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Title | X-RAY STUDY OF HUMAN SERUM ALBUMIN COMPLEXED WITH HEME | ||||||
Components | SERUM ALBUMIN | ||||||
Keywords | PLASMA PROTEIN | ||||||
Function / homology | Function and homology information cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wardell, M. / Wang, Z. / Ho, J.X. / Robert, J. / Ruker, F. / Ruble, J. / Carter, D.C. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2002 Title: The Atomic Structure of Human Methemalbumin at 1.9 A Authors: Wardell, M. / Wang, Z. / Ho, J.X. / Robert, J. / Ruker, F. / Ruble, J. / Carter, D.C. #1: Journal: Nature / Year: 1992 Title: Atomic Structure and Chemistry of Human Serum Albumin Authors: He, X.M. / Carter, D.C. #2: Journal: Science / Year: 1990 Title: Structure of Human Serum Albumin Authors: Carter, D.C. / He, X.M. #3: 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. #4: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n5u.cif.gz | 134.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n5u.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 1n5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/1n5u ftp://data.pdbj.org/pub/pdb/validation_reports/n5/1n5u | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768 | ||||
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#2: Chemical | ChemComp-MYR / #3: Chemical | ChemComp-HEM / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 50.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 3350, potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal grow | *PLUS Method: unknown / Details: Carter, D.C., (1994) Eur. J. Biochem., 226, 1049. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 8, 2001 | |||||||||
Radiation | Monochromator: SINGLE CRYSTAL, CYLINDRICALLY B / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. obs: 45420 / % possible obs: 90.3 % / Observed criterion σ(F): -3 / Redundancy: 2.89 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.043 | |||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.11 % / Rmerge(I) obs: 0.298 / % possible all: 68.3 | |||||||||
Reflection | *PLUS Highest resolution: 1.9 Å / % possible obs: 83.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.037 | |||||||||
Reflection shell | *PLUS Highest resolution: 1.9 Å / % possible obs: 56.3 % / Rmerge(I) obs: 0.266 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.81 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.3643 Å2 / ksol: 0.375589 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→45.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.228 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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