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- PDB-2ggj: The mutant Y218C of Deinococcus Radiodurans N-acylamino acid racemase -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ggj | |||||||||
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Title | The mutant Y218C of Deinococcus Radiodurans N-acylamino acid racemase | |||||||||
![]() | N-acylamino acid racemase | |||||||||
![]() | ISOMERASE / N-Acylamino Acid Racemase / Deinococcus Radiodurans | |||||||||
Function / homology | ![]() o-succinylbenzoate synthase / O-succinylbenzoate synthase activity / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / menaquinone biosynthetic process / isomerase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Wang, W.C. / Chiu, W.C. | |||||||||
![]() | ![]() 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 | ![]() | 292.1 KB | Display | ![]() |
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PDB format | ![]() | 237.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.5 KB | Display | ![]() |
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Full document | ![]() | 469.1 KB | Display | |
Data in XML | ![]() | 57.9 KB | Display | |
Data in CIF | ![]() | 83.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gggC ![]() 2gghC ![]() 2ggiC ![]() 2ggkC ![]() 2gglC ![]() 1r0mS 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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2 | ![]()
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Unit cell |
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Details | The biological assembly is a octamer. |
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Components
#1: Protein | Mass: 41000.633 Da / Num. of mol.: 4 / Mutation: Y218C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: CCRC 12827 / Plasmid: pQE30 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: lithium sulfate, Tris-HCl, PEG4000, pH 8.5, 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: Nov 12, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 55568 / % possible obs: 99.7 % |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1R0M Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.859 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.251 / 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: 16.743 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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