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Yorodumi- PDB-2yic: Crystal structure of the SucA domain of Mycobacterium smegmatis a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yic | ||||||
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Title | Crystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase (triclinic form) | ||||||
Components | 2-OXOGLUTARATE DECARBOXYLASE | ||||||
Keywords | LYASE | ||||||
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 / thiamine pyrophosphate binding / tricarboxylic acid cycle / magnesium ion binding Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM SMEGMATIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 | 2yic.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2yic.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 2yic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/2yic ftp://data.pdbj.org/pub/pdb/validation_reports/yi/2yic | HTTPS FTP |
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-Related structure data
Related structure data | 2xt6C 2xtaC 2y0pC 2yidC 2xt9 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
#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: MC2155 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: A0R2B1, 2-oxoglutarate decarboxylase #2: Chemical | ChemComp-TPP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Sequence details | FIRST GLY RESIDUE IS A PURIFICATI | |
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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: 2.74 Å3/Da / Density % sol: 55.2 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 46.5% MPD, 100 MM HEPES, PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 8, 2009 / Details: TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: CHANNEL CUT MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→49.5 Å / Num. obs: 263780 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 23.55 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.96→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XT9 2xt9 Resolution: 1.96→39.2 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.9108 / SU R Cruickshank DPI: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.148 / SU Rfree Blow DPI: 0.129 / SU Rfree Cruickshank DPI: 0.133 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=26355. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=26355. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
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Displacement parameters | Biso mean: 28.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.244 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→39.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.01 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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