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- PDB-5ein: Crystal structure of C148A mutant of LysY from Thermus thermophil... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ein | ||||||||||||
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Title | Crystal structure of C148A mutant of LysY from Thermus thermophilus in complex with NADP+ and LysW-gamma-aminoadipic acid | ||||||||||||
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![]() | OXIDOREDUCTASE/BIOSYNTHETIC PROTEIN / amino group-carrier-protein / lysine biosynthesis / GAPDH family / OXIDOREDUCTASE-BIOSYNTHETIC PROTEIN complex | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Shimizu, T. / Tomita, T. / Nishiyama, M. | ||||||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.2 KB | Display | ![]() |
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PDB format | ![]() | 136.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 35.4 KB | Display | |
Data in CIF | ![]() | 51.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5eioSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 38070.590 Da / Num. of mol.: 2 / Mutation: C148A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: argC2, argC, lysY, TT_C1542 / Production host: ![]() ![]() 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: 5957.581 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 579 molecules ![](data/chem/img/NAP.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, magnesium formate, NADP+, HEPES-NaOH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.7→50 Å / Num. obs: 75384 / % possible obs: 98.9 % / Redundancy: 5.5 % / Net I/σ(I): 38.1 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5EIO Resolution: 1.7→44.25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.213 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.111 / 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: 29.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→44.25 Å
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Refine LS restraints |
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