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- PDB-6npf: Structure of E.coli enolase in complex with an analog of the natu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6npf | ||||||
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Title | Structure of E.coli enolase in complex with an analog of the natural product SF-2312 metabolite. | ||||||
![]() | Enolase | ||||||
![]() | LYASE / Natural inhibitor / complex / enolase / SF2312 | ||||||
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. / Krucinska, J. / Lombardo, M. / Wright, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Functional and structural basis of E. coli enolase inhibition by SF2312: a mimic of the carbanion intermediate. Authors: Krucinska, J. / Lombardo, M.N. / Erlandsen, H. / Hazeen, A. / Duay, S.S. / Pattis, J.G. / Robinson, V.L. / May, E.R. / 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 | ![]() | 486.8 KB | Display | ![]() |
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PDB format | ![]() | 399 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 90.1 KB | Display | |
Data in CIF | ![]() | 123.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d3qSC 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 ABCDFE
#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 , 6 types, 276 molecules ![](data/chem/img/TLA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/KVM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/KVM.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2.1 M Ammonium Sulfate, 0.1 M MES buffer pH 6.0, 0.2 M Sodium/Potassium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 10, 2018 Details: Mirror: Flat bent collimating Rh coated mirror, toroidal focussing mirror |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.19499 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→93.03 Å / Num. obs: 97620 / % possible obs: 99.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 35.5 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.075 / Rrim(I) all: 0.106 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.57→2.62 Å / Redundancy: 2 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4421 / CC1/2: 0.791 / Rpim(I) all: 0.396 / Rrim(I) all: 0.56 / % possible all: 92.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6D3Q Resolution: 2.57→93.03 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.895 / SU B: 14.999 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 0.599 / ESU R Free: 0.311 / 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: 47.153 Å2
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Refinement step | Cycle: 1 / Resolution: 2.57→93.03 Å
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Refine LS restraints |
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