[English] 日本語
Yorodumi- PDB-4cqc: The reaction mechanism of the N-isopropylammelide isopropylaminoh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cqc | ||||||
---|---|---|---|---|---|---|---|
Title | The reaction mechanism of the N-isopropylammelide isopropylaminohydrolase AtzC: insights from structural and mutagenesis studies | ||||||
Components | N-ISOPROPYLAMMELIDE ISOPROPYL AMIDOHYDROLASE | ||||||
Keywords | HYDROLASE / ATRAZINE BREAKDOWN | ||||||
Function / homology | Function and homology information N-isopropylammelide isopropylaminohydrolase / N-isopropylammelide isopropylaminohydrolase activity / atrazine catabolic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | PSEUDOMONAS SP. ADP (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Balotra, S. / Newman, J. / French, N.G. / Peat, T.S. / Scott, C. | ||||||
Citation | Journal: Plos One / Year: 2015 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4cqc.cif.gz | 172.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4cqc.ent.gz | 134.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/4cqc ftp://data.pdbj.org/pub/pdb/validation_reports/cq/4cqc | HTTPS FTP |
---|
-Related structure data
Related structure data | 4cqbC 4cqdC 5akqC 2qt3S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 47101.590 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS SP. ADP (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O52063, EC: 3.5.99.4 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | N-TERMINAL HIS-TAG PLUS ONE MUTATION AT POSITION 219 | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.5 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 Details: PROTEIN AT 5.5 MG/ML OVER A RESERVOIR OF 2.5 M MALONATE PH 7.0, 100 MM HEPES BUFFER AT PH 7.5; DROPS WERE 150 NL PLUS 150 NL. IN-SITU THROMBIN TREATMENT WAS USED TO REMOVE THE HIS-TAG. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.008 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→46.3 Å / Num. obs: 51202 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.8 / % possible all: 98.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QT3 Resolution: 2.2→46.37 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.264 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 32.228 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→46.37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|