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Yorodumi- PDB-7c1c: Crystal structure of FumaraseC from Mannheimia succiniciproducens -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c1c | ||||||
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Title | Crystal structure of FumaraseC from Mannheimia succiniciproducens | ||||||
Components | Fumarate hydratase class II | ||||||
Keywords | LYASE / FumaraseC / Mannheimia succiniciproducens / succinate production / TCA cycle | ||||||
Function / homology | Function and homology information tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle Similarity search - Function | ||||||
Biological species | Mannheimia succiniciproducens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kim, B. / Lee, S.H. / Kim, K.-J. | ||||||
Citation | Journal: To Be Published Title: Structural and Biochemical analysis of FumaraseC from Mannheimia succiniciproducens Authors: Kim, B. / Lee, S.H. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c1c.cif.gz | 380.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c1c.ent.gz | 307.1 KB | Display | PDB format |
PDBx/mmJSON format | 7c1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/7c1c ftp://data.pdbj.org/pub/pdb/validation_reports/c1/7c1c | HTTPS FTP |
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-Related structure data
Related structure data | 7c1aC 7cvuC 7cvvC 7cvwC 7cvxC 1yfeS S: Starting model for refinement 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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-Components
#1: Protein | Mass: 50274.266 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mannheimia succiniciproducens (strain MBEL55E) (bacteria) Strain: MBEL55E / Gene: fumC, MS0760 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q65UJ3, fumarate hydratase #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.02 Å3/Da / Density % sol: 39.14 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop Details: 20% polyethylene glycol 3350, 0.2M Potassium fluoride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 240435 / % possible obs: 94.3 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.036 / Rrim(I) all: 0.091 / Χ2: 2.703 / Net I/σ(I): 11.2 / Num. measured all: 1457116 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YFE Resolution: 1.5→28.56 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.079 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.067 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 65.26 Å2 / Biso mean: 13.441 Å2 / Biso min: 7.44 Å2
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Refinement step | Cycle: final / Resolution: 1.5→28.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.538 Å / Rfactor Rfree error: 0
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