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- PDB-7kpe: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88Q mutant w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kpe | ||||||
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Title | Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88Q mutant with pyruvate bound in the active site and R,R-bislysine at the allosteric 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: THE ALLOSTERIC SITE RESIDUE, E88 INTERACTS WITH THE INHIBITORS TO TRANSMIT THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS BY FORMING A HYDROGEN BOND. Authors: Saran, S. / Majdi Yazdi, M. / Chung, I. / 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 | ![]() | 368.9 KB | Display | ![]() |
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PDB format | ![]() | 297.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 9.3 MB | Display | ![]() |
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Full document | ![]() | 9.5 MB | Display | |
Data in XML | ![]() | 78.6 KB | Display | |
Data in CIF | ![]() | 107.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kn9C ![]() 7knzC ![]() 7ko1C ![]() 7ko3C ![]() 7kocC ![]() 7kpcC ![]() 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 34184.273 Da / Num. of mol.: 6 / Mutation: E88Q 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, 1087 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/3VN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/3VN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ACT / #4: Chemical | #5: Chemical | ChemComp-PGE / #6: Chemical | #7: Chemical | #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: 2.41 Å3/Da / Density % sol: 48.89 % |
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Crystal grow | Temperature: 288.15 K / Method: microbatch / pH: 7.4 Details: 0.7 M Magnesium acetate, 10 % PEG 8000, 0.1 M Sodium acetate (pH 7.4), 120 mM R,R-bislysine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2019 |
Radiation | Monochromator: Single beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→45.88 Å / Num. obs: 122054 / % possible obs: 99.96 % / Redundancy: 15 % / CC1/2: 0.99 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.06→2.134 Å / Rmerge(I) obs: 0.237 / Num. unique obs: 12109 / % possible all: 99.92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LY8 Resolution: 2.06→45.88 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.44 / 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: 73.16 Å2 / Biso mean: 30.4247 Å2 / Biso min: 14.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.06→45.88 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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