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- PDB-6bfz: Crystal structure of enolase from E. coli with a mixture of apo f... -
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Basic information
Entry | Database: PDB / ID: 6bfz | ||||||
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Title | Crystal structure of enolase from E. coli with a mixture of apo form, substrate, and product form | ||||||
![]() | Enolase | ||||||
![]() | LYASE / Enolase / Escherichia coli / Apo / substrate / product | ||||||
Function / homology | ![]() bacterial degradosome / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / RNA catabolic process / RNA processing / glycolytic process / cytoskeleton / cell surface / magnesium ion binding ...bacterial degradosome / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / RNA catabolic process / RNA processing / glycolytic process / cytoskeleton / cell surface / magnesium ion binding / protein homodimerization activity / extracellular region / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Erlandsen, H. / Wright, D. / Krucinska, J. | ||||||
![]() | ![]() Title: Structural and Functional Studies of Bacterial Enolase, a Potential Target against Gram-Negative Pathogens. Authors: Krucinska, J. / Falcone, E. / Erlandsen, H. / Hazeen, A. / Lombardo, M.N. / Estrada, A. / Robinson, V.L. / Anderson, A.C. / Wright, D.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 504.1 KB | Display | ![]() |
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PDB format | ![]() | 408.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6bfyC ![]() 2fymS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABEFDC
#1: Protein | Mass: 47373.672 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: B7MLA0, UniProt: P0A6P9*PLUS, phosphopyruvate hydratase |
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-Non-polymers , 7 types, 705 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEP.gif)
![](data/chem/img/2PG.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEP.gif)
![](data/chem/img/2PG.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-PEP / | #6: Chemical | ChemComp-2PG / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2.0 M ammonium sulfate, 0.1 M MES, pH 6.0, 0.1 M sodium/potassium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2017 Details: White beam slits, double crystal Si(111) monochromator with horizontal theta-axis, tandem flat beam deflecting silicon mirrors (Pd and Si lanes), Kirkpatrick-Baez focusing silica mirrors, Pd- ...Details: White beam slits, double crystal Si(111) monochromator with horizontal theta-axis, tandem flat beam deflecting silicon mirrors (Pd and Si lanes), Kirkpatrick-Baez focusing silica mirrors, Pd-coated, each bent adaptively with 16 piezo actuators |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979186 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→29.69 Å / Num. obs: 165432 / % possible obs: 99.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.036 / Rrim(I) all: 0.051 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.21→2.24 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7139 / CC1/2: 0.786 / Rpim(I) all: 0.332 / Rrim(I) all: 0.47 / % possible all: 87.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2FYM Resolution: 2.21→29.69 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.078 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.176 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.171 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→29.69 Å
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Refine LS restraints |
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