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Yorodumi- PDB-1tkk: The Structure of a Substrate-Liganded Complex of the L-Ala-D/L-Gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tkk | ||||||
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Title | The Structure of a Substrate-Liganded Complex of the L-Ala-D/L-Glu Epimerase from Bacillus subtilis | ||||||
Components | similar to chloromuconate cycloisomerase | ||||||
Keywords | ISOMERASE / epimerase / enolase super family | ||||||
Function / homology | Function and homology information L-Ala-D/L-Glu epimerase activity / L-Ala-D/L-Glu epimerase / cell wall organization / cell wall macromolecule catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Klenchin, V.A. / Schmidt, D.M. / Gerlt, J.A. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Evolution of Enzymatic Activities in the Enolase Superfamily: Structure of a Substrate-Liganded Complex of the l-Ala-d/l-Glu Epimerase from Bacillus subtilis(,). Authors: Klenchin, V.A. / Schmidt, D.M. / 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 | 1tkk.cif.gz | 562.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tkk.ent.gz | 462.6 KB | Display | PDB format |
PDBx/mmJSON format | 1tkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/1tkk ftp://data.pdbj.org/pub/pdb/validation_reports/tk/1tkk | HTTPS FTP |
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-Related structure data
Related structure data | 1jpmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39519.582 Da / Num. of mol.: 8 / Fragment: YkfB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: Ykfb / Plasmid: pET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 16078363, UniProt: O34508*PLUS #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ALA / #4: Chemical | ChemComp-GLU / #5: 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: 2.43 Å3/Da / Density % sol: 49.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: The protein was concentrated to 20 mg/ml and dialyzed against 5 mM HEPES, 2 mM MgCl2, 50 mM NaCl, 0.25 mM TCEP, 1 mM NaN3, pH 7.0, drop frozen as small pellets in liquid nitrogen and stored ...Details: The protein was concentrated to 20 mg/ml and dialyzed against 5 mM HEPES, 2 mM MgCl2, 50 mM NaCl, 0.25 mM TCEP, 1 mM NaN3, pH 7.0, drop frozen as small pellets in liquid nitrogen and stored at -80 C. The frozen concentrated protein was thawed and diluted to 10 mg/mL with 5 mM HEPES, 2 mM MgCl2, 1 mM NaN3, pH 7.5. A stock solution of the peptide substrate L-Ala-L-Glu (Sigma) was neutralized to pH 7.5 with NaOH and brought to a final concentration of 1.6 M. This solution was added to the protein as 1/50th part by volume and the resultant mixture utilized for crystallization experiments. The initial crystals were grown by hanging drop by mixing 5 ?l of protein solution and 5 ?l of a solution containing 9-11% dimethyl-PEG 5000, 50 mM MOPS, 1% MPD, 1 mM NaN3, pH 7.0 and suspending the droplets over 600 ?l precipitant at 20 C, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Mar 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 173946 / Num. obs: 173946 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.6 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JPM Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.705 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.231 / 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: 25.435 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20 /
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