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Yorodumi- PDB-6i2q: Crystal structure of the wild-type SucA domain of Mycobacterium s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i2q | |||||||||
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Title | Crystal structure of the wild-type SucA domain of Mycobacterium smegmatis KGD (alpha-ketoglutarate decarboxylase), in complex with GarA | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / oxoglutarate dehydrogenase / 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 / mRNA binding / magnesium ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium smegmatis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Wagner, T. / Bellinzoni, M. / Alzari, P.M. | |||||||||
Citation | Journal: Sci.Signal. / Year: 2019 Title: Structural insights into the functional versatility of an FHA domain protein in mycobacterial signaling. Authors: Wagner, T. / Andre-Leroux, G. / Hindie, V. / Barilone, N. / Lisa, M.N. / Hoos, S. / Raynal, B. / Vulliez-Le Normand, B. / O'Hare, H.M. / Bellinzoni, 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 | 6i2q.cif.gz | 389.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i2q.ent.gz | 309.3 KB | Display | PDB format |
PDBx/mmJSON format | 6i2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i2q_validation.pdf.gz | 783.2 KB | Display | wwPDB validaton report |
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Full document | 6i2q_full_validation.pdf.gz | 788.3 KB | Display | |
Data in XML | 6i2q_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 6i2q_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/6i2q ftp://data.pdbj.org/pub/pdb/validation_reports/i2/6i2q | HTTPS FTP |
-Related structure data
Related structure data | 6i2pC 6i2rC 6i2sC 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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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 97166.648 Da / Num. of mol.: 1 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 |
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#2: Protein | Mass: 12112.292 Da / Num. of mol.: 1 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: garA, MSMEG_3647, MSMEI_3561 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QYG2 |
-Non-polymers , 4 types, 359 molecules
#3: Chemical | ChemComp-TPP / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-CA / |
#6: Water | ChemComp-HOH / |
-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: 55.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 100 mM Hepes-Na pH 7.0, 50% MPD |
-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: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→47.83 Å / Num. obs: 65695 / % possible obs: 98.9 % / Redundancy: 5 % / Biso Wilson estimate: 44.27 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.03 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.15→2.2 Å / Rmerge(I) obs: 0.747 / Rpim(I) all: 0.361 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YIC Resolution: 2.15→31.48 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.163 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.14
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Displacement parameters | Biso mean: 56.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.15→31.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.21 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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