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Yorodumi- PDB-6bfy: Crystal structure of enolase from Escherichia coli with bound 2-p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bfy | ||||||
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Title | Crystal structure of enolase from Escherichia coli with bound 2-phosphoglycerate substrate | ||||||
Components | Enolase | ||||||
Keywords | LYASE / Enolase / substrate / 2-phosphoglycerate / Escherichia coli | ||||||
Function / homology | Function and homology information bacterial degradosome / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / RNA catabolic process / RNA processing / glycolytic process / cytoskeleton / magnesium ion binding / cell surface ...bacterial degradosome / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / RNA catabolic process / RNA processing / glycolytic process / cytoskeleton / magnesium ion binding / cell surface / protein homodimerization activity / extracellular region / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Erlandsen, H. / Wright, D. / Krucinska, J. | ||||||
Citation | Journal: Biochemistry / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bfy.cif.gz | 513.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bfy.ent.gz | 417 KB | Display | PDB format |
PDBx/mmJSON format | 6bfy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/6bfy ftp://data.pdbj.org/pub/pdb/validation_reports/bf/6bfy | HTTPS FTP |
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-Related structure data
Related structure data | 6bfzC 2fymS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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 ABCFDE
#1: Protein | Mass: 47373.672 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: eno, ECS88_3047 / Production host: Escherichia coli (E. coli) References: UniProt: B7MLA0, UniProt: P0A6P9*PLUS, phosphopyruvate hydratase |
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-Non-polymers , 5 types, 1146 molecules
#2: Chemical | ChemComp-2PG / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.14 % |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1949 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 19, 2017 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: 1.1949 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→78.61 Å / Num. obs: 283200 / % possible obs: 100 % / Redundancy: 4 % / Biso Wilson estimate: 17.49 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.062 / Rrim(I) all: 0.132 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.81→1.84 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 13929 / CC1/2: 0.813 / Rpim(I) all: 0.349 / Rrim(I) all: 0.702 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FYM Resolution: 1.81→78.61 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.101 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.19 Å2
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Refinement step | Cycle: 1 / Resolution: 1.81→78.61 Å
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Refine LS restraints |
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