[English] 日本語
Yorodumi- PDB-3n4d: Crystal structure of Cg10062 inactivated by(R)-oxirane-2-carboxylate -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n4d | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Cg10062 inactivated by(R)-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: 2.54 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3n4d.cif.gz | 276.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3n4d.ent.gz | 226.3 KB | Display | PDB format |
PDBx/mmJSON format | 3n4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n4d_validation.pdf.gz | 506.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3n4d_full_validation.pdf.gz | 555.9 KB | Display | |
Data in XML | 3n4d_validation.xml.gz | 60.7 KB | Display | |
Data in CIF | 3n4d_validation.cif.gz | 80.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/3n4d ftp://data.pdbj.org/pub/pdb/validation_reports/n4/3n4d | HTTPS FTP |
-Related structure data
Related structure data | 3n4gC 3n4hC 2fltS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17203.256 Da / Num. of mol.: 9 / Fragment: Cg10062 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 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.23 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 4 Details: 6 micro liter hanging drop consisting of equal volume of crystallization solution (0.07 M sodium aetate buffer, pH 4.6, 1.4 M sodium chloride) and protein solution (18.9mg/L Cg10062 in 10mM ...Details: 6 micro liter hanging drop consisting of equal volume of crystallization solution (0.07 M sodium aetate buffer, pH 4.6, 1.4 M sodium chloride) and protein solution (18.9mg/L Cg10062 in 10mM Tris-SO4, pH 8.0), Hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 7, 2005 |
Radiation | Monochromator: BLUE MAX-FLUX OPTICAL SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. obs: 89329 / % possible obs: 99.9 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 61.2 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 1.206 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FLT Resolution: 2.54→45 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 36.627 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.54→45 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.54→2.606 Å / Total num. of bins used: 20
|