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Yorodumi- PDB-6r2d: Crystal structure of the SucA domain of Mycobacterium smegmatis K... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r2d | ||||||
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Title | Crystal structure of the SucA domain of Mycobacterium smegmatis KGD after soaking with succinylphosphonate phosphonoethyl ester, followed by temperature increase | ||||||
Components | Multifunctional 2-oxoglutarate metabolism enzyme | ||||||
Keywords | OXIDOREDUCTASE / oxoglutarate dehydrogenase / TPP-dependent decarboxylase | ||||||
Function / homology | Function and homology information 2-hydroxy-3-oxoadipate synthase / 2-oxoglutarate decarboxylase / 2-oxoglutarate decarboxylase activity / 2-hydroxy-3-oxoadipate synthase activity / oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding ...2-hydroxy-3-oxoadipate synthase / 2-oxoglutarate decarboxylase / 2-oxoglutarate decarboxylase activity / 2-hydroxy-3-oxoadipate synthase activity / oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding / tricarboxylic acid cycle / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Wagner, T. / Alzari, P.M. / Bellinzoni, M. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2019 Title: Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts. Authors: Wagner, T. / Boyko, A. / Alzari, P.M. / Bunik, V.I. / Bellinzoni, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r2d.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6r2d.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6r2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r2d_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6r2d_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6r2d_validation.xml.gz | 115.7 KB | Display | |
Data in CIF | 6r2d_validation.cif.gz | 165.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/6r2d ftp://data.pdbj.org/pub/pdb/validation_reports/r2/6r2d | HTTPS FTP |
-Related structure data
Related structure data | 6r29C 6r2aC 6r2bC 6r2cC 2yicS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 97166.648 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: kgd, sucA, MSMEG_5049, MSMEI_4922 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0R2B1, 2-hydroxy-3-oxoadipate synthase, 2-oxoglutarate decarboxylase, oxoglutarate dehydrogenase (succinyl-transferring), dihydrolipoyllysine-residue succinyltransferase #2: Chemical | ChemComp-ZP1 / ( #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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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: 2.66 Å3/Da / Density % sol: 53.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 58% MPD, 22.5 mM Na acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→80.57 Å / Num. obs: 172011 / % possible obs: 97.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 55.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.038 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8537 / CC1/2: 0.804 / Rpim(I) all: 0.321 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2YIC Resolution: 2.3→33.44 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.314 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.298 / SU Rfree Blow DPI: 0.212 / SU Rfree Cruickshank DPI: 0.219
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Displacement parameters | Biso mean: 58.43 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→33.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.32 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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