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- PDB-5m4b: Alpha-amino epsilon-caprolactam racemase D210A mutant in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m4b | ||||||
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Title | Alpha-amino epsilon-caprolactam racemase D210A mutant in complex with PLP and geminal diamine intermediate | ||||||
![]() | 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 | ![]() | 103 KB | Display | ![]() |
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PDB format | ![]() | 76.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805.5 KB | Display | ![]() |
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Full document | ![]() | 811.8 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 32.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m46C ![]() 5m49C ![]() 5m4dC ![]() 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46002.309 Da / Num. of mol.: 1 / Mutation: D210A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: N6UXY4, 2-aminohexano-6-lactam racemase |
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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: 2.01 Å3/Da / Density % sol: 38.95 % |
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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 2M / Detector: PIXEL / Date: Nov 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→45.79 Å / Num. obs: 57829 / % possible obs: 99.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 0.22 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZUK Resolution: 1.5→45.79 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.065 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.065 / 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: 16.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→45.79 Å
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Refine LS restraints |
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