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Yorodumi- PDB-7d2r: Crystal structure of Agrobacterium tumefaciens aconitase X mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d2r | ||||||
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Title | Crystal structure of Agrobacterium tumefaciens aconitase X mutant - S449C/C510V | ||||||
Components | cis-3-hydroxy-L-proline dehydratase | ||||||
Keywords | LYASE / cis-3-hydroxy-L-proline dehydratase | ||||||
Function / homology | FE2/S2 (INORGANIC) CLUSTER Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å | ||||||
Authors | Murase, Y. / Watanabe, Y. / Watanabe, S. | ||||||
Citation | Journal: Commun Biol / Year: 2021 Title: Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily. Authors: Watanabe, S. / Murase, Y. / Watanabe, Y. / Sakurai, Y. / Tajima, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d2r.cif.gz | 122.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d2r.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 7d2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/7d2r ftp://data.pdbj.org/pub/pdb/validation_reports/d2/7d2r | HTTPS FTP |
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-Related 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: 60648.082 Da / Num. of mol.: 1 / Mutation: S449C, C510V Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-FES / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, sodium chloride, Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→45.404 Å / Num. obs: 59959 / % possible obs: 99.6 % / Redundancy: 3.484 % / Biso Wilson estimate: 40.168 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.095 / Χ2: 1.113 / Net I/σ(I): 9.67 / Num. measured all: 208868 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.005→45.404 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.55 / 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: 89.64 Å2 / Biso mean: 37.8307 Å2 / Biso min: 18.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.005→45.404 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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