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- PDB-5msd: Structure of the A domain of carboxylic acid reductase (CAR) from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5msd | ||||||
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Title | Structure of the A domain of carboxylic acid reductase (CAR) from Nocardia iowensis in complex with AMP and benzoic acid | ||||||
![]() | Carboxylic acid reductase | ||||||
![]() | OXIDOREDUCTASE / adenylation domain / carboxylic acid reductase | ||||||
Function / homology | ![]() carboxylate reductase (NADP+) / aryl-aldehyde dehydrogenase (NADP+) activity / long-chain fatty acid-CoA ligase activity / : / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / phosphopantetheine binding / NADP binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dunstan, M.S. / Leys, D. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.6 KB | Display | ![]() |
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PDB format | ![]() | 119 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 784.8 KB | Display | ![]() |
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Full document | ![]() | 791.7 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 45.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mscSC ![]() 5msoC ![]() 5mspC ![]() 5msrC ![]() 5mssC ![]() 5mstC ![]() 5msuC ![]() 5msvC ![]() 5mswC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 128479.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q6RKB1, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor, carboxylate reductase (NADP+) |
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#2: Chemical | ChemComp-AMP / |
#3: Chemical | ChemComp-BEZ / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→29.061 Å / Num. obs: 63656 / % possible obs: 95 % / Redundancy: 2.1 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MSC Resolution: 1.71→29.061 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→29.061 Å
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Refine LS restraints |
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LS refinement shell |
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