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- PDB-5m4d: Alpha-amino epsilon-caprolactam racemase K241A mutant in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m4d | ||||||
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Title | Alpha-amino epsilon-caprolactam racemase K241A mutant in complex with D-ACL (external aldimine) | ||||||
![]() | Aminotransferase class-III | ||||||
![]() | ISOMERASE / PLP / racemase | ||||||
Function / homology | ![]() L-alanine catabolic process, by transamination / alanine-glyoxylate transaminase activity / glyoxylate catabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Frese, A. / Sutton, P.W. / Turkenburg, J.P. / Grogan, G. | ||||||
![]() | ![]() Title: Snapshots of the Catalytic Cycle of the Industrial Enzyme alpha-Amino-epsilon-Caprolactam Racemase (ACLR) Observed Using X-ray Crystallography Authors: Frese, A. / Sutton, P.W. / Turkenburg, J.P. / Grogan, 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 | ![]() | 96.4 KB | Display | ![]() |
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PDB format | ![]() | 71.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 870.6 KB | Display | ![]() |
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Full document | ![]() | 874.7 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m46C ![]() 5m49C ![]() 5m4bC ![]() 2zukS C: citing same article ( S: Starting model for refinement |
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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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 45860.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-7F7 / [ | ||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.91 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M MgCl2, 25 % PEG 3350, 0.1 mM HEPES (pH 7.0). |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→55.27 Å / Num. obs: 29415 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 1.3 |
Reflection shell | Resolution: 1.86→1.91 Å / Rmerge(I) obs: 0.88 / Num. unique all: 2171 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZUK Resolution: 1.93→55.27 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.368 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.181 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.423 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→55.27 Å
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Refine LS restraints |
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