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Yorodumi- PDB-6bol: Crystal structure of mutant 2-methylcitrate synthase mcsAG419A fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bol | ||||||
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Title | Crystal structure of mutant 2-methylcitrate synthase mcsAG419A from Aspergillus fumigatus. | ||||||
Components | 2-methylcitrate synthase, mitochondrial | ||||||
Keywords | TRANSFERASE / mcsA / 2-methylcitrate synthase / citrate synthase | ||||||
Function / homology | Function and homology information 2-methylcitrate synthase / 2-methylcitrate synthase activity / propionate catabolic process, 2-methylcitrate cycle / citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / tricarboxylic acid cycle / mitochondrial matrix Similarity search - Function | ||||||
Biological species | Neosartorya fumigata (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Schlachter, C. / Chruszcz, M. | ||||||
Citation | Journal: Biol.Chem. / Year: 2019 Title: Comparative studies of Aspergillus fumigatus 2-methylcitrate synthase and human citrate synthase. Authors: Schlachter, C.R. / Klapper, V. / Radford, T. / Chruszcz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bol.cif.gz | 341.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bol.ent.gz | 278 KB | Display | PDB format |
PDBx/mmJSON format | 6bol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/6bol ftp://data.pdbj.org/pub/pdb/validation_reports/bo/6bol | HTTPS FTP |
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-Related structure data
Related structure data | 5uqoC 5uqqC 5uqrC 5uqsC 5uquC 5uzpC 5uzqC 5uzrC 6bomC 6bonC 6booC 6bopC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 32 - 463 / Label seq-ID: 8 - 439
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-Components
#1: Protein | Mass: 48571.453 Da / Num. of mol.: 2 / Mutation: G419A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) (mold) Strain: CEA10 / CBS 144.89 / FGSC A1163 / Gene: mcsA, AFUB_094700 / Production host: Escherichia coli (E. coli) References: UniProt: B0YD89, 2-methylcitrate synthase, citrate synthase (unknown stereospecificity) #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 2.29 Å3/Da / Density % sol: 46.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Tris pH 7.5 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 47254 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.072 / Rrim(I) all: 0.186 / Rsym value: 0.249 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 2.97 / Num. unique obs: 2298 / Rpim(I) all: 0.308 / Rrim(I) all: 0.738 / Rsym value: 0.872 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.892 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.243 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.218 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→40 Å
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Refine LS restraints |
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