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Yorodumi- PDB-1i71: HIGH RESOLUTION CRYSTAL STRUCTURE OF APOLIPOPROTEIN(A) KRINGLE IV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i71 | ||||||
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Title | HIGH RESOLUTION CRYSTAL STRUCTURE OF APOLIPOPROTEIN(A) KRINGLE IV TYPE 7: INSIGHTS INTO LIGAND BINDING | ||||||
Components | APOLIPOPROTEIN(A) | ||||||
Keywords | HYDROLASE / alipoprotein(a) / kringle / protein-ligand interaction / lysine binding | ||||||
Function / homology | Function and homology information plasma lipoprotein particle / LDL remodeling / blood circulation / lipid transport / endopeptidase inhibitor activity / apolipoprotein binding / fibronectin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / lipid metabolic process / heparin binding ...plasma lipoprotein particle / LDL remodeling / blood circulation / lipid transport / endopeptidase inhibitor activity / apolipoprotein binding / fibronectin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / lipid metabolic process / heparin binding / endopeptidase activity / signaling receptor binding / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Ye, Q. / Rahman, M.N. / Koschinsky, M.L. / Jia, Z. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: High-resolution crystal structure of apolipoprotein(a) kringle IV type 7: insights into ligand binding. Authors: Ye, Q. / Rahman, M.N. / Koschinsky, M.L. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i71.cif.gz | 31.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i71.ent.gz | 20.5 KB | Display | PDB format |
PDBx/mmJSON format | 1i71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/1i71 ftp://data.pdbj.org/pub/pdb/validation_reports/i7/1i71 | HTTPS FTP |
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-Related structure data
Related structure data | 1pk4S 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: 9778.745 Da / Num. of mol.: 1 Fragment: RECOMBINANT KRINGLE IV TYPE 7 (RESIDUES 3781-3863) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET16B / Production host: Escherichia coli (E. coli) References: UniProt: P08519, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.38 Å3/Da / Density % sol: 48.27 % | |||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Ammonium sulfate, 2-[N-morpholino]ethane sulfonic acid, , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||
Crystal grow | *PLUS PH range low: 6 / PH range high: 5.5 | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9479 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2000 / Details: synchrotron optics |
Radiation | Monochromator: CHESS A1 optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9479 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→25 Å / Num. all: 48859 / Num. obs: 48859 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.069 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1070 / Rsym value: 0.239 / % possible all: 96.7 |
Reflection | *PLUS Num. obs: 15774 / % possible obs: 91.8 % / Num. measured all: 48859 / Rmerge(I) obs: 0.069 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PK4 Resolution: 1.45→6 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.45→6 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 6 Å / σ(F): 0 / Rfactor obs: 0.171 / Rfactor Rfree: 0.196 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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