[English] 日本語
Yorodumi- PDB-5msc: Structure of the A domain of carboxylic acid reductase (CAR) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5msc | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the A domain of carboxylic acid reductase (CAR) from Nocardia iowensis in complex with AMP | ||||||
Components | Carboxylic acid reductase | ||||||
Keywords | OXIDOREDUCTASE / adenylation domain / carboxylic acid reductase | ||||||
Function / homology | Function and homology information carboxylate reductase (NADP+) / aryl-aldehyde dehydrogenase (NADP+) activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / organonitrogen compound biosynthetic process / phosphopantetheine binding / lipid metabolic process / NADP binding / ATP binding Similarity search - Function | ||||||
Biological species | Nocardia iowensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Dunstan, M.S. / Leys, D. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Structures of carboxylic acid reductase reveal domain dynamics underlying catalysis. Authors: Gahloth, D. / Dunstan, M.S. / Quaglia, D. / Klumbys, E. / Lockhart-Cairns, M.P. / Hill, A.M. / Derrington, S.R. / Scrutton, N.S. / Turner, N.J. / Leys, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5msc.cif.gz | 152.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5msc.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 5msc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/5msc ftp://data.pdbj.org/pub/pdb/validation_reports/ms/5msc | HTTPS FTP |
---|
-Related structure data
Related structure data | 5msdC 5msoC 5mspC 5msrC 5mssC 5mstC 5msuC 5msvC 5mswC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 128479.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nocardia iowensis (bacteria) / Gene: car / Production host: Escherichia coli (E. coli) References: UniProt: Q6RKB1, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor, carboxylate reductase (NADP+) |
---|---|
#2: Chemical | ChemComp-AMP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: Crystals of A domain CARni (30mg/ml) were obtained using the sitting-drop vapour-diffusion and grew within 7 days at 4 degrees in 0.12 M ethylene glycols 0.1 M Tris-Bicine pH 8.5 30% glycerol/PEG 4K |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→43.52 Å / Num. obs: 59592 / % possible obs: 96.4 % / Redundancy: 3.4 % / CC1/2: 1 / Net I/σ(I): 12.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D_120002932 Resolution: 1.85→43.52 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.43
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→43.52 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|