[English] 日本語
Yorodumi- PDB-5lti: Crystal structure of the alpha subunit of heme dependent oxidativ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lti | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the alpha subunit of heme dependent oxidative N-demethylase (HODM) in complex with the dimethylamine substrate | ||||||
Components | heme dependent oxidative N-demethylase | ||||||
Keywords | OXIDOREDUCTASE / heme binding / PAS domain / amine oxidase / dimethylamine | ||||||
Function / homology | Haem-dependent oxidative N-demethylase, alpha subunit-like / Haem-dependent oxidative N-demethylase, alpha subunit-like / metal ion binding / DIMETHYLAMINE / PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / DI(HYDROXYETHYL)ETHER / DUF3445 domain-containing protein Function and homology information | ||||||
Biological species | Pseudomonas mendocina (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Ortmayer, M. / Leys, D. | ||||||
Citation | Journal: Nature / Year: 2016 Title: An oxidative N-demethylase reveals PAS transition from ubiquitous sensor to enzyme. Authors: Ortmayer, M. / Lafite, P. / Menon, B.R. / Tralau, T. / Fisher, K. / Denkhaus, L. / Scrutton, N.S. / Rigby, S.E. / Munro, A.W. / Hay, S. / Leys, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5lti.cif.gz | 89.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5lti.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 5lti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/5lti ftp://data.pdbj.org/pub/pdb/validation_reports/lt/5lti | HTTPS FTP |
---|
-Related structure data
Related structure data | 5lteSC 5lthC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40161.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: Pmen_3455 / Production host: Escherichia coli (E. coli) / References: UniProt: A4XXY9 |
---|
-Non-polymers , 6 types, 198 molecules
#2: Chemical | ChemComp-HEM / |
---|---|
#3: Chemical | ChemComp-DMN / |
#4: Chemical | ChemComp-NO / |
#5: Chemical | ChemComp-PEG / |
#6: Chemical | ChemComp-NA / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.52 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: The HODM-heme subunit was crystallised at 3 mg ml-1 in 50 mM KPi, 100 mM KCl, pH 7.5. Initial crystallisation conditions were identified using the JCSG+ matrix screen (Molecular dimensions). ...Details: The HODM-heme subunit was crystallised at 3 mg ml-1 in 50 mM KPi, 100 mM KCl, pH 7.5. Initial crystallisation conditions were identified using the JCSG+ matrix screen (Molecular dimensions). Crystals suitable for diffraction experiments were obtained by sitting drop vapour diffusion at 277 K in 400 nL drops containing equal volumes of protein and a solution containing 30% PEG 2K MME and 0.1 M potassium thiocyanate. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 26, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→28.36 Å / Num. obs: 36266 / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 12 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5LTE Resolution: 1.9→28.36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.325 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.824 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→28.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|