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- PDB-6boo: Crystal structure of 2-methylcitrate synthase from Aspergillus fu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6boo | ||||||
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Title | Crystal structure of 2-methylcitrate synthase from Aspergillus fumigatus with oxaloacetate and coenzyme-A. | ||||||
![]() | 2-methylcitrate synthase, mitochondrial | ||||||
![]() | TRANSFERASE / mcsA / 2-methylcitrate synthase / citrate synthase | ||||||
Function / homology | ![]() 2-methylcitrate synthase / 2-methylcitrate synthase activity / propionate catabolic process, 2-methylcitrate cycle / citrate synthase (unknown stereospecificity) / citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schlachter, C. / Chruszcz, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 660.7 KB | Display | ![]() |
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PDB format | ![]() | 548.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 61.4 KB | Display | |
Data in CIF | ![]() | 83.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uqoSC ![]() 5uqqC ![]() 5uqrC ![]() 5uqsC ![]() 5uquC ![]() 5uzpC ![]() 5uzqC ![]() 5uzrC ![]() 6bolC ![]() 6bomC ![]() 6bonC ![]() 6bopC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 31 - 465 / Label seq-ID: 7 - 441
NCS ensembles :
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Components
#1: Protein | Mass: 48557.426 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: CEA10 / CBS 144.89 / FGSC A1163 / Gene: mcsA, AFUB_094700 / Production host: ![]() ![]() References: UniProt: B0YD89, 2-methylcitrate synthase, citrate synthase (unknown stereospecificity) #2: Chemical | ChemComp-OAA / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris pH 6.5 28% PEGMME2000 1.0 mM oxaloacetate 1.0 mM coenzyme-A |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Aug 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 47339 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.056 / Rrim(I) all: 0.103 / Rsym value: 0.068 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 2362 / Rpim(I) all: 0.346 / Rrim(I) all: 0.622 / Rsym value: 0.437 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5UQO Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / ESU R Free: 0.359 / 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: 42.361 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→40 Å
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Refine LS restraints |
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