+Open data
-Basic information
Entry | Database: PDB / ID: 3kiv | |||||||||
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Title | RECOMBINANT KRINGLE IV-10/M66 VARIANT OF HUMAN APOLIPOPROTEIN(A) | |||||||||
Components | APOLIPOPROTEIN | |||||||||
Keywords | KRINGLE / LYSINE BINDING SITE / APOLIPOPROTEIN(A) | |||||||||
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 / serine-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 3kiv.cif.gz | 32.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kiv.ent.gz | 20.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/3kiv ftp://data.pdbj.org/pub/pdb/validation_reports/ki/3kiv | 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: 9169.012 Da / Num. of mol.: 1 / Fragment: KRINGLE IV-10 Source method: isolated from a genetically manipulated source Details: KIV-10/T66 VARIANT OF HUMAN APOLIPOPROTEIN(A) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P08519 |
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#2: Chemical | ChemComp-ACA / |
#3: Water | ChemComp-HOH / |
Compound details | N-TERMINAL (VR) AND C-TERMINAL (SDTEGTV) INTERKRINGULAR PARTS ARE DISORDERED. THE P30 RESIDUE IS IN ...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: 1.76 Å3/Da / Density % sol: 30.6 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||
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 / 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: 1.8→23 Å / Num. obs: 5656 / % possible obs: 81 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.8→2 Å / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 4.7 / % possible all: 53 |
Reflection | *PLUS Num. measured all: 12758 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 2 Å / % possible obs: 53 % / Rmerge(I) obs: 0.101 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→9 Å / σ(F): 1
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Displacement parameters | Biso mean: 15.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→9 Å
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Refine LS restraints |
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Software | *PLUS Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |