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- PDB-5tjy: Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Myco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tjy | ||||||
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Title | Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with 2,6 Pyridine Dicarboxylic Acid and NADH | ||||||
![]() | 4-hydroxy-tetrahydrodipicolinate reductase | ||||||
![]() | OXIDOREDUCTASE / Lysine Biosynthesis | ||||||
Function / homology | ![]() 4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mank, N. / Arnette, K. / Klapper, V. / Chruszcz, M. | ||||||
![]() | ![]() Title: Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus. Authors: Pote, S. / Kachhap, S. / Mank, N.J. / Daneshian, L. / Klapper, V. / Pye, S. / Arnette, A.K. / Shimizu, L.S. / Borowski, T. / Chruszcz, 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 | ![]() | 70.2 KB | Display | ![]() |
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PDB format | ![]() | 48.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796.1 KB | Display | ![]() |
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Full document | ![]() | 798.1 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tejC ![]() 5tekC ![]() 5temC ![]() 5tenC ![]() 5tjzC ![]() 5ugvC ![]() 5us6C ![]() 1c3vS C: citing same article ( S: Starting model for refinement |
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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 , 1 types, 1 molecules A
#1: Protein | Mass: 25682.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25177 / H37Ra / Gene: dapB, MRA_2798 / Production host: ![]() ![]() References: UniProt: A5U6C6, 4-hydroxy-tetrahydrodipicolinate reductase |
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-Non-polymers , 10 types, 140 molecules ![](data/chem/img/PDC.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BEZ.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BEZ.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PDC / | ||||
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#3: Chemical | ChemComp-NAI / | ||||
#4: Chemical | ChemComp-SO4 / | ||||
#5: Chemical | ChemComp-BEZ / | ||||
#6: Chemical | ChemComp-IMD / | ||||
#7: Chemical | ChemComp-PG4 / | ||||
#8: Chemical | ChemComp-NA / | ||||
#9: Chemical | ChemComp-EDO / #10: Chemical | ChemComp-CL / | #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 50 mM Ammonium Sulfate, 50 mM Bis-Tris pH 6.5, 30% v/v Pentaerythritol ethoxylate (15/4 EO/OH) |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cryostream | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→40 Å / Num. obs: 13744 / % possible obs: 99.9 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.023 / Rrim(I) all: 0.105 / Χ2: 1.164 / Net I/av σ(I): 38.478 / Net I/σ(I): 7.3 / Num. measured all: 282237 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1C3V Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.696 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.19 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.3 Å2 / Biso mean: 43.662 Å2 / Biso min: 26.92 Å2
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Refinement step | Cycle: final / Resolution: 2.4→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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