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- PDB-8rp4: Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis (D1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rp4 | ||||||
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Title | Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis (D156A mutant) | ||||||
![]() | Alpha-methylacyl-CoA racemase | ||||||
![]() | ISOMERASE / CoA-transferase / epimerization / CoA-transferase family III / alpha proton exchange / homo dimer | ||||||
Function / homology | ![]() alpha-methylacyl-CoA racemase / alpha-methylacyl-CoA racemase activity / acyl-CoA metabolic process / lipid metabolic process / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mojanaga, O.O. / Acharya, K.R. / Lloyd, M.D. | ||||||
Funding support | Botswana, 1items
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![]() | ![]() Title: alpha-Methylacyl-CoA Racemase from Mycobacterium tuberculosis -Detailed Kinetic and Structural Characterization of the Active Site. Authors: Mojanaga, O.O. / Woodman, T.J. / Lloyd, M.D. / Acharya, K.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.5 KB | Display | ![]() |
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PDB format | ![]() | 220.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8rmwC ![]() 8rp3C ![]() 8rp5C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39114.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: O06543, alpha-methylacyl-CoA racemase #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.70480084 Å3/Da / Density % sol: 54.55 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 20 % (v/v) ethylene glycol, 10 % (w/v) PEG 8000, 0.1 M sodium HEPES-MOPS, |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 23, 2023 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.64→90.173 Å / Num. obs: 99692 / % possible obs: 99 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.058 / Rrim(I) all: 0.11 / Net I/σ(I): 9.9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.835 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→90.173 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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