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Yorodumi- PDB-7xky: Crystal structure of Methanocaldococcus jannaschii two-subunit Fu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xky | |||||||||
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Title | Crystal structure of Methanocaldococcus jannaschii two-subunit Fumarate hydratase apo-protein complex | |||||||||
Components | (Fumarate hydrataseFumarase) x 2 | |||||||||
Keywords | LYASE / Apo-protein / Class-I fumarase / two-subunit fumarase / thioredoxin-like | |||||||||
Function / homology | Function and homology information fumarate hydratase / hydro-lyase activity / 4 iron, 4 sulfur cluster binding / lyase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Methanocaldococcus jannaschii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å | |||||||||
Authors | Bellur, A. / Jayaraman, V. / Balaram, H. | |||||||||
Funding support | India, 2items
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Citation | Journal: Biochemistry / Year: 2023 Title: Revisiting the Burden Borne by Fumarase: Enzymatic Hydration of an Olefin. Authors: Bellur, A. / Das, S. / Jayaraman, V. / Behera, S. / Suryavanshi, A. / Balasubramanian, S. / Balaram, P. / Jindal, G. / Balaram, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xky.cif.gz | 101.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xky.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 7xky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/7xky ftp://data.pdbj.org/pub/pdb/validation_reports/xk/7xky | HTTPS FTP |
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-Related structure data
Related structure data | 5dniC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32852.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: HA335_00100 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A832SUM4, fumarate hydratase |
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#2: Protein | Mass: 22223.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: HA335_03165 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A832WL32 |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.61 % |
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Crystal grow | Temperature: 297 K / Method: microbatch Details: 0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→69.62 Å / Num. obs: 17961 / % possible obs: 98.4 % / Redundancy: 7.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.124 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.46→2.59 Å / Rmerge(I) obs: 0.525 / Num. unique obs: 2578 / CC1/2: 0.871 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.46→52.13 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.187 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.529 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.066 Å2
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Refinement step | Cycle: 1 / Resolution: 2.46→52.13 Å
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