+Open data
-Basic information
Entry | Database: PDB / ID: 8rmw | ||||||
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Title | Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis. | ||||||
Components | Alpha-methylacyl-CoA racemase | ||||||
Keywords | ISOMERASE / CoA-transferase / epimerization / CoA-transferase family III / alpha proton exchange / homo dimer | ||||||
Function / homology | Function and homology information alpha-methylacyl-CoA racemase / alpha-methylacyl-CoA racemase activity / formyl-CoA transferase / formyl-CoA transferase activity / : Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Mojanaga, O.O. / Acharya, K.R. / Lloyd, M.D. | ||||||
Funding support | Botswana, 1items
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Citation | Journal: Biomolecules / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rmw.cif.gz | 278.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rmw.ent.gz | 218.9 KB | Display | PDB format |
PDBx/mmJSON format | 8rmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rmw_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
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Full document | 8rmw_full_validation.pdf.gz | 459.6 KB | Display | |
Data in XML | 8rmw_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 8rmw_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/8rmw ftp://data.pdbj.org/pub/pdb/validation_reports/rm/8rmw | HTTPS FTP |
-Related structure data
Related structure data | 8rp3C 8rp4C 8rp5C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39158.324 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: frc_2, frc, frc_3, mcr, DSI46_17980, ERS007679_00285, ERS007681_01258, ERS007720_00852, ERS007722_01391, ERS053720_03198, F6W99_03855, GJE03_06060, SAMEA2683035_02587 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A045IZ15, formyl-CoA transferase, alpha-methylacyl-CoA racemase #2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.74398351 Å3/Da / Density % sol: 55.2 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å | |||||||||||||||||||||
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: 1.65→90.471 Å / Num. obs: 100251 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.057 / Rrim(I) all: 0.108 / Net I/σ(I): 8.9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→90.471 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.177 / SU B: 3.133 / SU ML: 0.095 / Average fsc free: 0.9452 / Average fsc work: 0.9557 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.094 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: 30.979 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→90.471 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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