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- PDB-2xt6: Crystal structure of Mycobacterium smegmatis alpha-ketoglutarate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xt6 | ||||||
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Title | Crystal structure of Mycobacterium smegmatis alpha-ketoglutarate decarboxylase homodimer (orthorhombic form) | ||||||
![]() | 2-OXOGLUTARATE DECARBOXYLASE | ||||||
![]() | LYASE / KDH / KGD | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wagner, T. / Bellinzoni, M. / Wehenkel, A.M. / O'Hare, H.M. / Alzari, P.M. | ||||||
![]() | ![]() Title: Functional Plasticity and Allosteric Regulation of Alpha-Ketoglutarate Decarboxylase in Central Mycobacterial Metabolism. Authors: Wagner, T. / Bellinzoni, M. / Wehenkel, A.M. / O'Hare, H.M. / Alzari, P.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 815.8 KB | Display | ![]() |
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PDB format | ![]() | 661.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xtaC ![]() 2y0pC ![]() 2yicC ![]() 2yidC ![]() 2xt9 ![]() 2xt5 ![]() 2xt7 ![]() 2xt8 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9623, -0.2124, -0.1697), Vector: |
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Components
#1: Protein | Mass: 124096.305 Da / Num. of mol.: 2 / Fragment: RESIDUES 116-1227 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | FIRST GLY RESIDUE IS A PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.7 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 39% MPD, 100 MM HEPES, PH 7.0, 200 MM NACL |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 26, 2009 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS |
Radiation | Monochromator: CHANNEL CUT MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→82 Å / Num. obs: 79835 / % possible obs: 99.3 % / Observed criterion σ(I): 2.4 / Redundancy: 3.5 % / Biso Wilson estimate: 75.02 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.74→2.89 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.4 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XT9 ![]() 2xt9 Resolution: 2.74→40.12 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.8741 / SU R Cruickshank DPI: 0.508 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.48 / SU Rfree Blow DPI: 0.267 / SU Rfree Cruickshank DPI: 0.274
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Displacement parameters | Biso mean: 70.04 Å2
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Refine analyze | Luzzati coordinate error obs: 0.377 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.74→40.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.74→2.81 Å / Total num. of bins used: 20
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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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