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Yorodumi- PDB-5eio: Crystal structure of LysY from Thermus thermophilus complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eio | ||||||
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Title | Crystal structure of LysY from Thermus thermophilus complexed with NADP+ and LysW-gamma-aminoadipic semialdehyde | ||||||
Components |
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Keywords | OXIDOREDUCTASE/BIOSYNTHETIC PROTEIN / amino group-carrier-protein / lysine biosynthesis / GAPDH family / OXIDOREDUCTASE-BIOSYNTHETIC PROTEIN complex | ||||||
Function / homology | Function and homology information N-acetyl-gamma-aminoadipyl-phosphate reductase activity / [amino-group carrier protein]-6-phospho-L-2-aminoadipate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / lysine biosynthetic process via aminoadipic acid / arginine biosynthetic process / NADP+ binding / NAD binding / protein dimerization activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Shimizu, T. / Tomita, T. / Nishiyama, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Crystal Structure of the LysYLysW Complex from Thermus thermophilus. Authors: Shimizu, T. / Tomita, T. / 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 | 5eio.cif.gz | 166.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eio.ent.gz | 131 KB | Display | PDB format |
PDBx/mmJSON format | 5eio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/5eio ftp://data.pdbj.org/pub/pdb/validation_reports/ei/5eio | HTTPS FTP |
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-Related structure data
Related structure data | 5einC 2ozpS 3wwlS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein , 2 types, 3 molecules ABC
#1: Protein | Mass: 38102.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: argC2, argC, lysY, TT_C1542 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): CodonPlus RIL References: UniProt: O50146, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor, N-acetyl-gamma-glutamyl-phosphate reductase #2: Protein | | Mass: 5814.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: orfF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): CodonPlus RIL / References: UniProt: Q9ZND7 |
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-Non-polymers , 4 types, 408 molecules
#3: Chemical | #4: Chemical | ChemComp-ACY / #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 2000 MME, calcium acetate, NADP, HEPES-NaOH |
-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: Feb 8, 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: 1.8→50 Å / Num. obs: 64110 / % possible obs: 99.4 % / Redundancy: 5.5 % / Rsym value: 0.112 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OZP, 3WWL Resolution: 1.8→36.37 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.734 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.125 / 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: 32.617 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→36.37 Å
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Refine LS restraints |
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