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Yorodumi- PDB-1r6w: Crystal structure of the K133R mutant of o-Succinylbenzoate synth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r6w | ||||||
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Title | Crystal structure of the K133R mutant of o-Succinylbenzoate synthase (OSBS) from Escherichia coli. Complex with SHCHC | ||||||
Components | o-Succinylbenzoate Synthase | ||||||
Keywords | LYASE / Enolase superfamily / TIM barrel / capping alpha+beta domain | ||||||
Function / homology | Function and homology information o-succinylbenzoate synthase / O-succinylbenzoate synthase activity / hydro-lyase activity / menaquinone biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Klenchin, V.A. / Taylor Ringia, E.A. / Gerlt, J.A. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Evolution of Enzymatic Activity in the Enolase Superfamily: Structural and Mutagenic Studies of the Mechanism of the Reaction Catalyzed by o-Succinylbenzoate Synthase from Escherichia coli Authors: Klenchin, V.A. / Taylor Ringia, E.A. / Gerlt, J.A. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r6w.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r6w.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 1r6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/1r6w ftp://data.pdbj.org/pub/pdb/validation_reports/r6/1r6w | HTTPS FTP |
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-Related structure data
Related structure data | 1fhvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35765.734 Da / Num. of mol.: 1 / Mutation: K133R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P29208, Lyases; Carbon-oxygen lyases; Hydro-lyases |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-164 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.2 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 5.5 Details: The K133R mutant of OSBS was concentrated to 15 mg/ml, dialyzed against 5 mM Tris pH 8.3 containing 2 mM MgCl2, drop frozen as small pellets in liquid nitrogen and stored at -80 C. Crystals ...Details: The K133R mutant of OSBS was concentrated to 15 mg/ml, dialyzed against 5 mM Tris pH 8.3 containing 2 mM MgCl2, drop frozen as small pellets in liquid nitrogen and stored at -80 C. Crystals were grown at 20 C by small-scale batch experiments by combining 15 ml of protein solution and 15 ml of a solution containing 12-13% MePEG 5000, 100 mM sodium acetate, 60 mM MgCl2, at pH 5.5. SHCHC was included in the crystallization at a final concentration of approximately 2.5 mM., microbatch, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: batch method | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.979 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→31 Å / Num. all: 43694 / Num. obs: 43694 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 41 |
Reflection shell | Resolution: 1.62→1.68 Å / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 17.1 / % possible all: 98.9 |
Reflection | *PLUS Lowest resolution: 31.3 Å / % possible obs: 99.8 % / Redundancy: 7.05 % / Num. measured all: 307914 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1fhv Resolution: 1.62→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.489 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.085 / ESU R Free: 0.086 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.66 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Rfactor Rfree: 0.2 / Rfactor Rwork: 0.167 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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