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Yorodumi- PDB-3n4h: Crystal structure of Cg10062 inactivated by (S)-oxirane-2-carboxylate -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n4h | ||||||
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Title | Crystal structure of Cg10062 inactivated by (S)-oxirane-2-carboxylate | ||||||
Components | Putative tautomerase | ||||||
Keywords | HYDROLASE / Cg10062 / cis-3-Chloroacrylic Acid Dehalogenase / Tautomerase superfamily / Beta-alpha-beta motif | ||||||
Function / homology | Tautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / Tautomerase cis-CaaD-like domain-containing protein Function and homology information | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Guo, Y. / Robertson, B.A. / Hackert, M.L. / Whitman, C.P. | ||||||
Citation | Journal: To be Published Title: Crystal Structures of the Native and Inactivated Cg10062, a cis-3-Chloroacrylic Acid Dehalogenase from Corynebacterium glutamicum: Implications for the Evolution of cis-3-Chloroacrylic Acid ...Title: Crystal Structures of the Native and Inactivated Cg10062, a cis-3-Chloroacrylic Acid Dehalogenase from Corynebacterium glutamicum: Implications for the Evolution of cis-3-Chloroacrylic Acid Dehalogenase Activity in the Tautomerase Superfamily Authors: Guo, Y. / Robertson, B.A. / J Poelarends, G. / Thunnissen, A.-M.W.H. / Hackert, M.L. / Whitman, C.P. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n4h.cif.gz | 40.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n4h.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 3n4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/3n4h ftp://data.pdbj.org/pub/pdb/validation_reports/n4/3n4h | HTTPS FTP |
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-Related structure data
Related structure data | 3n4dC 3n4gSC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17203.256 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg0081, Cg10062, Cgl0062 / Plasmid: pET3b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) References: UniProt: Q8NU77, Hydrolases; Acting on halide bonds; In carbon-halide compounds |
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#2: 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: 1.64 Å3/Da / Density % sol: 25.18 % |
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Crystal grow | Temperature: 298 K / pH: 4 Details: 6 micro liter hanging drop consisting of equal volume of crystallization solution (3% PEG 6000, pH 4.0) and protein solution (18.1mg/L Cg10062 in 10mM Tris-SO4, pH 8.0), vapor diffusion, ...Details: 6 micro liter hanging drop consisting of equal volume of crystallization solution (3% PEG 6000, pH 4.0) and protein solution (18.1mg/L Cg10062 in 10mM Tris-SO4, pH 8.0), vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 4, 2005 |
Radiation | Monochromator: BLUE MAX-FLUX OPTICAL SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. obs: 7841 / % possible obs: 99.8 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 64.887 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 8.6 / Num. unique all: 766 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3N4G Resolution: 2.02→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0 / SU B: 8.932 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.186 / 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 max: 86.23 Å2 / Biso mean: 35.552 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.073 Å / Total num. of bins used: 20
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