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- PDB-7klt: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N mutant w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7klt | ||||||
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Title | Dihydrodipicolinate synthase (DHDPS) from C.jejuni, H59N mutant with pyruvate bound in the active site | ||||||
![]() | 4-hydroxy-tetrahydrodipicolinate synthase | ||||||
![]() | LYASE / Dihydrodipicolinate synthase | ||||||
Function / homology | ![]() (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Saran, S. / Sanders, D.A.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: H59 PLAYS THE MOST VITAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS ENZYME Authors: Saran, S. / Skovpen, Y. / Majdi Yazdi, M. / Palmer, D.R.J. / Sanders, D.A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 365.3 KB | Display | ![]() |
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PDB format | ![]() | 297.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 15.2 MB | Display | ![]() |
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Full document | ![]() | 15.2 MB | Display | |
Data in XML | ![]() | 73.2 KB | Display | |
Data in CIF | ![]() | 99.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7klqC ![]() 7klsC ![]() 7klyC ![]() 7km0C ![]() 7km1C ![]() 4ly8S 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 34161.215 Da / Num. of mol.: 6 / Mutation: H59N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700819 / NCTC 11168 / Gene: dapA, Cj0806 / Production host: ![]() ![]() References: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase |
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-Non-polymers , 8 types, 747 molecules ![](data/chem/img/PG4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PG4 / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PGE / #6: Chemical | ChemComp-ACT / #7: Chemical | ChemComp-PEG / #8: Chemical | ChemComp-GOL / #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.99 % |
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Crystal grow | Temperature: 288.15 K / Method: microbatch / pH: 7.4 Details: 0.5 M Magnesium acetate, 8 % PEG8000, 0.1 M Sodium acetate (pH 7.4), 60 mM L-Lysine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2017 |
Radiation | Monochromator: Double beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→44.14 Å / Num. obs: 142117 / % possible obs: 99.8 % / Redundancy: 15 % / CC1/2: 0.998 / Net I/σ(I): 12.06 |
Reflection shell | Resolution: 1.97→2.04 Å / Rmerge(I) obs: 0.9167 / Num. unique obs: 14129 / % possible all: 99.96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LY8 Resolution: 1.97→44.14 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.97 / 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: 73.64 Å2 / Biso mean: 34.8545 Å2 / Biso min: 18.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.97→44.14 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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