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Yorodumi- PDB-2y05: Crystal structure of human leukotriene B4 12-hydroxydehydrogenase... -
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-Basic information
Entry | Database: PDB / ID: 2y05 | ||||||
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Title | Crystal structure of human leukotriene B4 12-hydroxydehydrogenase in complex with NADP and raloxifene | ||||||
Components | PROSTAGLANDIN REDUCTASE 1 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information 2-alkenal reductase (NADPH) activity / leukotriene B4 metabolic process / 13-lipoxin reductase activity / leukotriene B4 12-hydroxy dehydrogenase activity / lipoxin A4 metabolic process / 2-alkenal reductase [NAD(P)+] / 13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-oxidase [NAD(P)+] activity / : / Synthesis of Lipoxins (LX) ...2-alkenal reductase (NADPH) activity / leukotriene B4 metabolic process / 13-lipoxin reductase activity / leukotriene B4 12-hydroxy dehydrogenase activity / lipoxin A4 metabolic process / 2-alkenal reductase [NAD(P)+] / 13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-oxidase [NAD(P)+] activity / : / Synthesis of Lipoxins (LX) / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / prostaglandin metabolic process / extracellular exosome / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yue, W.W. / Shafqat, N. / Krojer, T. / Pike, A.C.W. / von Delft, F. / Sethi, R. / Savitsky, P. / Johansson, C. / Arrowsmith, C. / Weigelt, J. ...Yue, W.W. / Shafqat, N. / Krojer, T. / Pike, A.C.W. / von Delft, F. / Sethi, R. / Savitsky, P. / Johansson, C. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Leukotriene B4 12-Hydroxydehydrogenase in Complex with Nadp and Raloxifene Authors: Yue, W.W. / Shafqat, N. / Krojer, T. / Pike, A.C.W. / von Delft, F. / Sethi, R. / Savitsky, P. / Johansson, C. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y05.cif.gz | 270.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y05.ent.gz | 219.5 KB | Display | PDB format |
PDBx/mmJSON format | 2y05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y05_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 2y05_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 2y05_validation.xml.gz | 52.3 KB | Display | |
Data in CIF | 2y05_validation.cif.gz | 72 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/2y05 ftp://data.pdbj.org/pub/pdb/validation_reports/y0/2y05 | HTTPS FTP |
-Related structure data
Related structure data | 1zsvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 2 - 329 / Label seq-ID: 1 - 328
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35757.516 Da / Num. of mol.: 4 / Fragment: MDR DOMAIN, RESIDUES 4-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: Q14914, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor, 13,14-dehydro-15-oxoprostaglandin 13-reductase, 2-alkenal reductase [NAD(P)+] |
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-Non-polymers , 5 types, 458 molecules
#2: Chemical | ChemComp-NAP / #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-EDO / #6: 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: 2.75 Å3/Da / Density % sol: 55.34 % / Description: NONE |
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Crystal grow | Details: 10% PEG 10K, 8% ETGLY, 0.1M HEPES, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 24, 2008 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→59.5 Å / Num. obs: 82606 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.6 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZSV Resolution: 2.2→59.55 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.943 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.235 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→59.55 Å
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Refine LS restraints |
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