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Yorodumi- PDB-2jlc: Crystal structure of E.coli MenD, 2-succinyl-5-enolpyruvyl-6-hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jlc | ||||||
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Title | Crystal structure of E.coli MenD, 2-succinyl-5-enolpyruvyl-6-hydroxy- 3-cyclohexadiene-1-carboxylate synthase - native protein | ||||||
Components | 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE / MENAQUINONE BIOSYNTHESIS / MANGANESE / THIAMINE DIPHOSPHATE COFACTOR / THIAMINE PYROPHOSPHATE | ||||||
Function / homology | Function and homology information 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 / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Dawson, A. / Fyfe, P.K. / Hunter, W.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Specificity and Reactivity in Menaquinone Biosynthesis: The Structure of Escherichia Coli Mend (2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3-Cyclohexadiene-1-Carboxylate Synthase). Authors: Dawson, A. / Fyfe, P.K. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jlc.cif.gz | 230 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jlc.ent.gz | 182.4 KB | Display | PDB format |
PDBx/mmJSON format | 2jlc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/2jlc ftp://data.pdbj.org/pub/pdb/validation_reports/jl/2jlc | HTTPS FTP |
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-Related structure data
Related structure data | 2jlaSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 63846.348 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET15BTEV_ECMEND / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) References: UniProt: P17109, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | SEQUENCE INCLUDES N-TERMINAL HIS TAG AND TEV CLEAVAGE SITE | |
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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: 2.3 Å3/Da / Density % sol: 46.5 % / Description: NONE |
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Crystal grow | pH: 8 Details: 100 MM SODIUM CITRATE PH 5.6, 8 % ISO-PROPANOL AND 14 % PEG 6K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→92.8 Å / Num. obs: 42932 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.5 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JLA Resolution: 2.5→92.85 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.863 / SU B: 10.275 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.735 / ESU R Free: 0.355 / 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 / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→92.85 Å
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Refine LS restraints |
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