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- PDB-5dds: Crystal structure of aminotransferase CrmG from Actinoalloteichus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dds | |||||||||
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Title | Crystal structure of aminotransferase CrmG from Actinoalloteichus sp. WH1-2216-6 in complex with PLP | |||||||||
![]() | CrmG | |||||||||
![]() | TRANSFERASE / Aminotransferase / PLP / Caerulomycin A | |||||||||
Function / homology | ![]() transaminase activity / pyridoxal phosphate binding / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Xu, J. / Feng, Z. / Liu, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Biochemical and Structural Insights into the Aminotransferase CrmG in Caerulomycin Biosynthesis Authors: Zhu, Y. / Xu, J. / Mei, X. / Feng, Z. / Zhang, L. / Zhang, Q. / Zhang, G. / Zhu, W. / Liu, J. / Zhang, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 387.6 KB | Display | ![]() |
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PDB format | ![]() | 328 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 494.9 KB | Display | ![]() |
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Full document | ![]() | 514.1 KB | Display | |
Data in XML | ![]() | 67.8 KB | Display | |
Data in CIF | ![]() | 92.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 57219.520 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #2: Chemical | ChemComp-PLP / #3: Chemical | #4: Chemical | ChemComp-ACY / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.56 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Sodium acetate, 0.1M TRIS pH 8.5, 32% PEG3350, 2% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.6→69.92 Å / Num. obs: 61697 / % possible obs: 92.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.4 | |||||||||||||||
Reflection shell | Resolution: 2.6→2.66 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.3 / % possible all: 89.5 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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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 max: 122.36 Å2 / Biso mean: 33.739 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 2.6→62.02 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.6→2.6 Å / Total num. of bins used: 20 |