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- PDB-2x7j: Structure of the menaquinone biosynthesis protein MenD from Bacil... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x7j | ||||||
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Title | Structure of the menaquinone biosynthesis protein MenD from Bacillus subtilis | ||||||
![]() | 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE | ||||||
![]() | TRANSFERASE / METAL-BINDING | ||||||
Function / homology | ![]() 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity / menaquinone biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dawson, A. / Chen, M. / Fyfe, P.K. / Guo, Z. / Hunter, W.N. | ||||||
![]() | ![]() Title: Structure and Reactivity of Bacillus Subtilis Mend Catalyzing the First Committed Step in Menaquinone Biosynthesis. Authors: Dawson, A. / Chen, M. / Fyfe, P.K. / Guo, Z. / Hunter, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 478.8 KB | Display | ![]() |
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PDB format | ![]() | 387.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 96.2 KB | Display | |
Data in CIF | ![]() | 134.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 66954.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P23970, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase |
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-Non-polymers , 6 types, 1098 molecules ![](data/chem/img/TPP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-TPP / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | ADDITIONAL RESIDUES AT N-TERMINUS ARE DUE TO HEXA-HIS TAG, TEV CLEAVAGE SITE AND THREE RESIDUES ...ADDITIONAL |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.8 % / Description: NONE |
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Crystal grow | pH: 8 Details: PROTEIN BUFFER CONTAINED 20 MM TRIS, 50 MM NACL, PH 7.5. CRYSTALLISATION CONDITION CONTAINED 35% PEG 1.5K, 0.1 M TRIS PH 8, 0.25 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 17, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0064 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→68.84 Å / Num. obs: 101958 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.35→62.14 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.104 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY. STRUCTURE WAS SOLVED USING SAD ON A SEMET DERIVATISED PROTEIN. THE SEMET REFINEMENT WAS NOT COMPLETED OR SUBMITTED.
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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: 32.448 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→62.14 Å
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Refine LS restraints |
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