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Yorodumi- PDB-2xta: Crystal structure of the SucA domain of Mycobacterium smegmatis a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xta | ||||||
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Title | Crystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase in complex with acetyl-CoA (triclinic form) | ||||||
Components | 2-OXOGLUTARATE DECARBOXYLASE | ||||||
Keywords | LYASE / KDH / KGD | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wagner, T. / Bellinzoni, M. / Wehenkel, A.M. / O'Hare, H.M. / Alzari, P.M. | ||||||
Citation | Journal: Chem.Biol. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xta.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2xta.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 2xta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xta_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 2xta_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 2xta_validation.xml.gz | 113.1 KB | Display | |
Data in CIF | 2xta_validation.cif.gz | 160.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/2xta ftp://data.pdbj.org/pub/pdb/validation_reports/xt/2xta | HTTPS FTP |
-Related structure data
Related structure data | 2xt6C 2y0pC 2yicC 2yidC 2xt9 2xt5 2xt7 2xt8 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 97166.648 Da / Num. of mol.: 4 / Fragment: RESIDUES 361-1227 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: A0R2B1, 2-oxoglutarate decarboxylase |
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-Non-polymers , 5 types, 757 molecules
#2: Chemical | ChemComp-TPP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CA / #5: Chemical | #6: 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: 2.79 Å3/Da / Density % sol: 55.9 % / Description: NONE |
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Crystal grow | pH: 7.6 / Details: 54% MPD, 25 MM SODIUM ACETATE, pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9799 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2009 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DUAL CHANNEL CUT CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9799 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→78.1 Å / Num. obs: 187791 / % possible obs: 92.6 % / Observed criterion σ(I): 2.2 / Redundancy: 2 % / Biso Wilson estimate: 36.62 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.2→2.31 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / % possible all: 88.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XT9 2xt9 Resolution: 2.2→78.11 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9207 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.223 / SU Rfree Blow DPI: 0.173 / SU Rfree Cruickshank DPI: 0.179
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Displacement parameters | Biso mean: 43.83 Å2
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Refine analyze | Luzzati coordinate error obs: 0.299 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→78.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 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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