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- PDB-5akq: X-ray structure and mutagenesis studies of the N-isopropylammelid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5akq | ||||||
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Title | X-ray structure and mutagenesis studies of the N-isopropylammelide isopropylaminohydrolase, AtzC | ||||||
![]() | N-ISOPROPYLAMMELIDE ISOPROPYL AMIDOHYDROLASE | ||||||
![]() | HYDROLASE / ATRAZINE DEGRADATION / ENZYME EVOLUTION | ||||||
Function / homology | ![]() N-isopropylammelide isopropylaminohydrolase / N-isopropylammelide isopropylaminohydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines / atrazine catabolic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Balotra, S. / Warden, A.C. / Newman, J. / Briggs, L.J. / Scott, C. / Peat, T.S. | ||||||
![]() | ![]() Title: X-Ray Structure and Mutagenesis Studies of the N-Isopropylammelide Isopropylaminohydrolase, Atzc Authors: Balotra, S. / Warden, A.C. / Newman, J. / Briggs, L.J. / Scott, C. / Peat, T.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 313.3 KB | Display | ![]() |
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PDB format | ![]() | 255.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438 KB | Display | ![]() |
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Full document | ![]() | 442.5 KB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 38.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cqbSC ![]() 4cqcC ![]() 4cqdC 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 47169.645 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: N-TERMINAL HIS-TAG WITH THROMBIN CLEAVAGE SITE ADDED TO THE FULL LENGTH ENZYME WITH THE N304D MUTATION Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.9 % / Description: NONE |
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Crystal grow | pH: 7 Details: 4.0 MG/ML PROTEIN; RESERVOIR WAS 2.56 M MALONATE AT PH 7.0; DROPS WERE 200 NL PLUS 200 NL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→46.2 Å / Num. obs: 30950 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4CQB Resolution: 2.6→110.5 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / SU B: 28.761 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.666 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 36.038 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→110.5 Å
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Refine LS restraints |
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