+Open data
-Basic information
Entry | Database: PDB / ID: 4kiv | ||||||
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Title | RECOMBINANT KRINGLE IV-10/W72R MUTANT OF HUMAN APOLIPOPROTEIN(A) | ||||||
Components | APOLIPOPROTEIN | ||||||
Keywords | LYSINE BINDING SITE / SITE MUTATION | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Mochalkin, I. / Tulinsky, A. / Scanu, A. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Recombinant kringle IV-10 modules of human apolipoprotein(a): structure, ligand binding modes, and biological relevance. Authors: Mochalkin, I. / Cheng, B. / Klezovitch, O. / Scanu, A.M. / Tulinsky, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kiv.cif.gz | 25.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kiv.ent.gz | 18.5 KB | Display | PDB format |
PDBx/mmJSON format | 4kiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/4kiv ftp://data.pdbj.org/pub/pdb/validation_reports/ki/4kiv | HTTPS FTP |
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-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: 9170.088 Da / Num. of mol.: 1 / Fragment: KRINGLE IV-10 / Mutation: W72R Source method: isolated from a genetically manipulated source Details: KIV-10/W72R MUTANT OF HUMAN APOLIPOPROTEIN(A) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P08519 |
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#2: Water | ChemComp-HOH / |
Compound details | N-TERMINAL (VR) AND C-TERMINAL (SDTEGTV) INTERKRINGULAR PARTS ARE DISORDERED. SIDE CHAIN FOR ...N-TERMINAL (VR) AND C-TERMINAL (SDTEGTV) INTERKRING |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.56 Å3/Da / Density % sol: 22 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MSC-YALE 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: 2.2→24.3 Å / Num. obs: 6494 / % possible obs: 64 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.2→2.5 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 2 / % possible all: 45 |
Reflection | *PLUS Num. obs: 2241 / Num. measured all: 6494 |
Reflection shell | *PLUS % possible obs: 45 % / Rmerge(I) obs: 0.089 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→7 Å / σ(F): 1
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Displacement parameters | Biso mean: 21.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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Refine LS restraints |
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Software | *PLUS Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.166 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |