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Yorodumi- PDB-6nz9: Crystal structure of E. coli fumarase C bound to citrate at 1.53 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nz9 | ||||||
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Title | Crystal structure of E. coli fumarase C bound to citrate at 1.53 angstrom resolution | ||||||
Components | Fumarate hydratase class II | ||||||
Keywords | LYASE / fumarase / inhibitor complex / metabolism / Krebs Cycle | ||||||
Function / homology | Function and homology information tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / tricarboxylic acid cycle / response to oxidative stress / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.528 Å | ||||||
Authors | Stuttgen, G.M. / May, J.F. / Bhattcharyya, B. / Weaver, T.M. | ||||||
Citation | Journal: Febs Lett. / Year: 2020 Title: Closed fumarase C active-site structures reveal SS Loop residue contribution in catalysis. Authors: Stuttgen, G.M. / Grosskopf, J.D. / Berger, C.R. / May, J.F. / Bhattacharyya, B. / Weaver, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nz9.cif.gz | 200.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nz9.ent.gz | 158.4 KB | Display | PDB format |
PDBx/mmJSON format | 6nz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/6nz9 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/6nz9 | HTTPS FTP |
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-Related structure data
Related structure data | 6nzaC 6nzbC 6nzcC 1fuoS 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: 51239.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: fumC, b1611, JW1603 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05042, fumarate hydratase #2: Chemical | ChemComp-CIT / #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: 2.45 Å3/Da / Density % sol: 49.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: PEG 3350, citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 1.528→63.553 Å / Num. obs: 146755 / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.528→1.55 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.975 / Num. unique obs: 7249 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FUO Resolution: 1.528→45.975 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.27 Å2 / Biso mean: 21.655 Å2 / Biso min: 9.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.528→45.975 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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