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- PDB-2ggk: The mutant A302C of Agrobacterium radiobacter N-carbamoyl-D-amino... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ggk | |||||||||
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Title | The mutant A302C of Agrobacterium radiobacter N-carbamoyl-D-amino-acid amidohydrolase | |||||||||
![]() | N-carbamoyl-D-amino acid amidohydrolase | |||||||||
![]() | HYDROLASE / N-Carbamoyl-D-Amino-Acid Amidohydrolase | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Wang, W.C. / Chiu, W.C. / You, J.Y. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 244.8 KB | Display | ![]() |
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PDB format | ![]() | 199 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.6 KB | Display | ![]() |
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Full document | ![]() | 476.7 KB | Display | |
Data in XML | ![]() | 46.6 KB | Display | |
Data in CIF | ![]() | 65.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gggC ![]() 2gghC ![]() 2ggiC ![]() 2ggjC ![]() 2gglC ![]() 1fo6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The crystal structure of D-NCAase A302C mutant reveals a tetramer with 222 symmetry. |
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Components
#1: Protein | Mass: 34241.125 Da / Num. of mol.: 4 / Mutation: A302C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q44185, N-carbamoyl-D-amino-acid hydrolase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.61 % |
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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 |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 17, 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: 2.3→30 Å / Num. obs: 56903 / % possible obs: 95.6 % |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 95.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FO6 Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.225 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.248 / 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 mean: 33.184 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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