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Open data
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Basic information
Entry | Database: PDB / ID: 7xll | ||||||
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Title | Alanine racemase from Lactobacillus sakei Uonuma-1. | ||||||
![]() | Alanine racemase | ||||||
![]() | ISOMERASE / alanine racemase / PLP-dependent enzyme | ||||||
Function / homology | ACETATE ION / ALANINE / DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shimizu-Ibuka, A. / Kato, Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: Regulation of alanine racemase activity by carboxylates and the d-type substrate d-alanine. Authors: Shimizu-Ibuka, A. / Sato, A. / Ichimura, H. / Hiraga, H. / Nakayama, S. / Nishiwaki, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 221 KB | Display | ![]() |
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PDB format | ![]() | 139.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476 KB | Display | ![]() |
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Full document | ![]() | 480.1 KB | Display | |
Data in XML | ![]() | 37.7 KB | Display | |
Data in CIF | ![]() | 57.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3e5pS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41952.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GB LC605911 / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-ALA / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.89 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 4000, Tris-HCl, sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→62.52 Å / Num. obs: 76568 / % possible obs: 99.7 % / Redundancy: 5.9 % / CC1/2: 0.992 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.76→1.79 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4267 / CC1/2: 0.794 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3E5P Resolution: 1.76→62.52 Å / SU ML: 0.1792 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4236 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.39 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→62.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.78 Å
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