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Yorodumi- PDB-6nzc: Crystal structure of E. coli fumarase C N326A variant with closed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nzc | ||||||
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Title | Crystal structure of E. coli fumarase C N326A variant with closed SS Loop at 1.40 angstrom resolution | ||||||
Components | Fumarate hydratase class II | ||||||
Keywords | LYASE / fumarase / metabolism / Krebs Cycle / citrate | ||||||
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: 1.403 Å | ||||||
Authors | Weaver, T.M. / May, J.F. / Bhattacharyya, B. | ||||||
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 | 6nzc.cif.gz | 376.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nzc.ent.gz | 304.6 KB | Display | PDB format |
PDBx/mmJSON format | 6nzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/6nzc ftp://data.pdbj.org/pub/pdb/validation_reports/nz/6nzc | HTTPS FTP |
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-Related structure data
Related structure data | 6nz9C 6nzaC 6nzbC 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: 51196.469 Da / Num. of mol.: 2 / Mutation: N326A 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 | #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: 2.43 Å3/Da / Density % sol: 49.47 % |
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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-F / Wavelength: 0.9787 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 13, 2018 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→108.7 Å / Num. obs: 187757 / % possible obs: 99.2 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.4→1.43 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9382 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FUO Resolution: 1.403→59.42 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.8 Å2 / Biso mean: 19.9713 Å2 / Biso min: 8.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.403→59.42 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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