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Yorodumi- PDB-5k2m: Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-g... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k2m | ||||||||||||
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Title | Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA | ||||||||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / ATP-dependent amine/thiol ligase family Amino-group carrier protein Lysine biosynthesis Arginine biosynthesis | ||||||||||||
Function / homology | Function and homology information coenzyme F420-2 alpha-glutamyl ligase activity / lysine biosynthetic process / ligase activity, forming carbon-nitrogen bonds / protein modification process => GO:0036211 / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||||||||
Authors | Yoshida, A. / Tomita, T. / Nishiyama, M. | ||||||||||||
Funding support | Japan, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2016 Title: Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System. Authors: Yoshida, A. / Tomita, T. / Atomi, H. / Kuzuyama, T. / Nishiyama, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k2m.cif.gz | 929.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k2m.ent.gz | 773.3 KB | Display | PDB format |
PDBx/mmJSON format | 5k2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k2m_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 5k2m_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 5k2m_validation.xml.gz | 90.9 KB | Display | |
Data in CIF | 5k2m_validation.cif.gz | 124.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/5k2m ftp://data.pdbj.org/pub/pdb/validation_reports/k2/5k2m | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 2 types, 14 molecules ABCDGHIJEFKLMN
#1: Protein | Mass: 30525.818 Da / Num. of mol.: 8 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: TK0278 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: Q5JFW0 #2: Protein | Mass: 5983.672 Da / Num. of mol.: 6 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: TK0279 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: Q5JFV9 |
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-Non-polymers , 7 types, 655 molecules
#3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-MG / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-UN1 / | #9: 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: 2.5 Å3/Da / Density % sol: 50.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: MPD, PEG 3350, Imidazole pH 6.5, Ammonium sulfate, AMP-PNP, AAA, MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 28, 2014 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→50 Å / Num. obs: 142143 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.18→2.22 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.388 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VPD, 3WWL Resolution: 2.18→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.879 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.186 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.18→50 Å
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Refine LS restraints |
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