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Yorodumi- PDB-4l6w: Carboxyltransferase subunit (AccD6) of Mycobacterium tuberculosis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l6w | ||||||
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Title | Carboxyltransferase subunit (AccD6) of Mycobacterium tuberculosis acetyl-CoA carboxylase | ||||||
Components | Probable propionyl-CoA carboxylase beta chain 6 | ||||||
Keywords | LIGASE / Crotonase fold / CoA binding | ||||||
Function / homology | Function and homology information acetyl-CoA carboxytransferase / Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / fatty acid elongation, saturated fatty acid / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / ligase activity / peptidoglycan-based cell wall / fatty acid biosynthetic process / transferase activity Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Anandhakrishnan, M. / Ehebauer, M.T. / Wilmanns, M. | ||||||
Citation | Journal: To be Published Title: Structural analysis of the carboxyltransferase subunit of Mycobacterium tuberculosis acetyl-CoA carboxylase Authors: Anandhakrishnan, M. / Ehebauer, M.T. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l6w.cif.gz | 327.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l6w.ent.gz | 264.2 KB | Display | PDB format |
PDBx/mmJSON format | 4l6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l6w_validation.pdf.gz | 439.4 KB | Display | wwPDB validaton report |
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Full document | 4l6w_full_validation.pdf.gz | 451.3 KB | Display | |
Data in XML | 4l6w_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 4l6w_validation.cif.gz | 45.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/4l6w ftp://data.pdbj.org/pub/pdb/validation_reports/l6/4l6w | HTTPS FTP |
-Related structure data
Related structure data | 2bzrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 52370.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: accD6, MT2307, MTCY427.28, Rv2247 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P63407, UniProt: P9WQH5*PLUS, acetyl-CoA carboxylase #2: 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: 2.56 Å3/Da / Density % sol: 52.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 27% (w/v) PEG 3350, 0.3 M ammonium sulphate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.2395 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2012 / Details: 25 Hz, 450 micron sensor thickness |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2395 Å / Relative weight: 1 |
Reflection | Resolution: 1.947→76.942 Å / Num. all: 79503 / Num. obs: 79385 / % possible obs: 99.85 % / Observed criterion σ(I): -3 / Redundancy: 12.88 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 34.4 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5.14 / Num. unique all: 12489 / % possible all: 98.59 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BZR Resolution: 1.95→68.97 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.337 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.222 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→68.97 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.947→1.998 Å / Total num. of bins used: 20
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