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Yorodumi- PDB-3cdk: Crystal structure of the co-expressed succinyl-CoA transferase A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cdk | ||||||
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Title | Crystal structure of the co-expressed succinyl-CoA transferase A and B complex from Bacillus subtilis | ||||||
Components |
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Keywords | TRANSFERASE / CO-EXPRESSED COMPLEX / HETERO-TETRAMER / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information 3-oxoacid CoA-transferase / succinyl-CoA:3-oxo-acid CoA-transferase activity / CoA-transferase activity / acetate CoA-transferase activity Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Kim, Y. / Zhou, M. / Stols, L. / Eschenfeldt, W. / Donnelly, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the co-expressed succinyl-CoA transferase A and B complex from Bacillus subtilis. Authors: Kim, Y. / Zhou, M. / Stols, L. / Eschenfeldt, W. / Donnelly, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cdk.cif.gz | 341 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cdk.ent.gz | 281 KB | Display | PDB format |
PDBx/mmJSON format | 3cdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/3cdk ftp://data.pdbj.org/pub/pdb/validation_reports/cd/3cdk | HTTPS FTP |
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-Related structure data
Related structure data | 1m3eS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25704.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: scoA, yxjD, BSU38990, N15K / Plasmid: pMCSG17 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42315, 3-oxoacid CoA-transferase #2: Protein | Mass: 23629.146 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: scoB, yxjE, BSU38980, N15L / Plasmid: pMCSG21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42316, 3-oxoacid CoA-transferase #3: 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: 2.33 Å3/Da / Density % sol: 47.13 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1M tri-Sodium citrate dihydrate pH 5.6, 20% Isopropanol, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2007 / Details: Mirrors |
Radiation | Monochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→48.3 Å / Num. all: 28084 / Num. obs: 28084 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.147 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.59→2.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.543 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1M3E Resolution: 2.59→48.3 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9 / SU B: 24.492 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Native data set has been used for structure determination.
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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: 53.745 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→48.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.66 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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