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Yorodumi- PDB-5ni4: Crystal structure of human LTA4H mutant E271A in complex with LTA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ni4 | ||||||
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Title | Crystal structure of human LTA4H mutant E271A in complex with LTA4 (crystal form II) | ||||||
Components | Leukotriene A-4 hydrolase | ||||||
Keywords | HYDROLASE / Metallopeptidase / epoxide hydrolase / leukotriene A4 | ||||||
Function / homology | Function and homology information leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase / tripeptide aminopeptidase activity / Biosynthesis of protectins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Synthesis of Leukotrienes (LT) and Eoxins (EX) ...leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase / tripeptide aminopeptidase activity / Biosynthesis of protectins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Synthesis of Leukotrienes (LT) and Eoxins (EX) / protein metabolic process / leukotriene biosynthetic process / epoxide hydrolase activity / type I pneumocyte differentiation / response to zinc ion / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / lipid metabolic process / response to peptide hormone / tertiary granule lumen / peptidase activity / ficolin-1-rich granule lumen / Neutrophil degranulation / proteolysis / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å | ||||||
Authors | Stsiapanava, A. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Capturing LTA4 hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB4 synthesis. Authors: Stsiapanava, A. / Samuelsson, B. / Haeggstrom, J.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ni4.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ni4.ent.gz | 930.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ni4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/5ni4 ftp://data.pdbj.org/pub/pdb/validation_reports/ni/5ni4 | HTTPS FTP |
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-Related structure data
Related structure data | 4dprC 5ni2SC 5ni6C 5niaC 5nidC 5nieC C: citing same article (ref.) 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: 70134.820 Da / Num. of mol.: 3 / Mutation: E271A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LTA4H, LTA4 / Plasmid: pT3MB4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P09960, leukotriene-A4 hydrolase #2: Chemical | #3: Chemical | ChemComp-IMD / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-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: 48.57 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 8% (w/v) PEG 20 000, 15% (w/v) PEG MME 550, 100 mM MES/imidazole pH 6.9, 20 mM of each alcohol (1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol) PH range: 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.895→49.81 Å / Num. obs: 152082 / % possible obs: 99.93 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.08 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1885 / Rpim(I) all: 0.08085 / Net I/σ(I): 6.61 |
Reflection shell | Resolution: 1.895→1.963 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.609 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 15217 / CC1/2: 0.351 / Rpim(I) all: 0.6945 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NI2 Resolution: 1.895→49.807 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.895→49.807 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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