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Open data
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Basic information
Entry | Database: PDB / ID: 4lus | ||||||
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Title | alanine racemase [Clostridium difficile 630] | ||||||
![]() | (Alanine racemase) x 2 | ||||||
![]() | ISOMERASE / Alanine racemase | ||||||
Function / homology | ![]() alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Asojo, O.A. | ||||||
![]() | ![]() Title: Structural and biochemical analyses of alanine racemase from the multidrug-resistant Clostridium difficile strain 630. Authors: Asojo, O.A. / Nelson, S.K. / Mootien, S. / Lee, Y. / Rezende, W.C. / Hyman, D.A. / Matsumoto, M.M. / Reiling, S. / Kelleher, A. / Ledizet, M. / Koski, R.A. / Anthony, K.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 314.9 KB | Display | ![]() |
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PDB format | ![]() | 253.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4lutC ![]() 4luyC ![]() 4a3qS 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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Components
#1: Protein | Mass: 43636.066 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Carboxylic modified Lysine / Source: (gene. exp.) ![]() ![]() #2: Protein | | Mass: 43593.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-TCE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.64 % |
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Crystal grow | Temperature: 298 K / pH: 7.5 Details: 20 mg/ml protein in 50mM Tris pH 8.0, 0.02% v/v BME, 10 micromolar pyridoxal-L-phosphate, crystallization buffer 1mM TCEP, 0.2M sodium formate, 20% w/V PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.076→54.54 Å / Num. obs: 93251 / % possible obs: 88.4 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.076→2.2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.9 / % possible all: 52.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4A3Q Resolution: 2.1→54.54 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.251 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 39.958 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→54.54 Å
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Refine LS restraints |
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