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Yorodumi- PDB-7cnr: Crystal structure of Thermococcus kodakaraensis aconitase X (apo-form) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cnr | ||||||
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Title | Crystal structure of Thermococcus kodakaraensis aconitase X (apo-form) | ||||||
Components |
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Keywords | LYASE / mevalonate 5-phosphate dehydratase | ||||||
Function / homology | Function and homology information phosphomevalonate dehydratase / 3 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.39 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 | 7cnr.cif.gz | 388.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cnr.ent.gz | 317.6 KB | Display | PDB format |
PDBx/mmJSON format | 7cnr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cnr_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7cnr_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7cnr_validation.xml.gz | 69.9 KB | Display | |
Data in CIF | 7cnr_validation.cif.gz | 94.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/7cnr ftp://data.pdbj.org/pub/pdb/validation_reports/cn/7cnr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42410.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1249 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JGJ6 #2: Protein | Mass: 13909.031 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea) Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1248 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JGJ7 #3: Chemical | ChemComp-F3S / Has ligand of interest | Y | |
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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: 3.1 Å3/Da / Density % sol: 60.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.39→49.312 Å / Num. obs: 74870 / % possible obs: 99.7 % / Redundancy: 6.648 % / Biso Wilson estimate: 85.829 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.187 / Rrim(I) all: 0.203 / Χ2: 1.187 / Net I/σ(I): 9.51 / Num. measured all: 497752 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.39→23.288 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.66 / 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: 198.01 Å2 / Biso mean: 94.9341 Å2 / Biso min: 52.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.39→23.288 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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