[English] 日本語
Yorodumi- PDB-2ggl: The mutant A222C of Agrobacterium radiobacter N-carbamoyl-D-amino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ggl | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The mutant A222C of Agrobacterium radiobacter N-carbamoyl-D-amino acid amidohydrolase | |||||||||
Components | N-carbamoyl-D-amino acid amidohydrolase | |||||||||
Keywords | HYDROLASE / N-Carbamoyl-D-Amino-Acid Amidohydrolase | |||||||||
Function / homology | Function and homology information N-carbamoyl-D-amino-acid hydrolase / N-carbamoyl-D-amino acid hydrolase activity / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity Similarity search - Function | |||||||||
Biological species | Agrobacterium tumefaciens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Wang, W.C. / Chiu, W.C. / You, J.Y. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structure-Stability-Activity Relationship in Covalently Cross-linked N-Carbamoyl d-Amino acid Amidohydrolase and N-Acylamino acid Racemase. Authors: Chiu, W.C. / You, J.Y. / Liu, J.S. / Hsu, S.K. / Hsu, W.H. / Shih, C.H. / Hwang, J.K. / Wang, W.C. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ggl.cif.gz | 247.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ggl.ent.gz | 201.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ggl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ggl_validation.pdf.gz | 449.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ggl_full_validation.pdf.gz | 474.1 KB | Display | |
Data in XML | 2ggl_validation.xml.gz | 48.5 KB | Display | |
Data in CIF | 2ggl_validation.cif.gz | 68.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/2ggl ftp://data.pdbj.org/pub/pdb/validation_reports/gg/2ggl | HTTPS FTP |
-Related structure data
Related structure data | 2gggC 2gghC 2ggiC 2ggjC 2ggkC 1fo6S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Details | The crystal structure of D-NCAase A222C mutant reveals a tetramer with 222 symmetry. |
-Components
#1: Protein | Mass: 34241.129 Da / Num. of mol.: 4 / Mutation: A222C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q44185, N-carbamoyl-D-amino-acid hydrolase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.08 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: lithium sulfate, HEPES buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 113 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 13, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 50489 / % possible obs: 94.8 % |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 93.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FO6 Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.977 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.243 / 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: 32.097 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
|