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- PDB-6kjj: Functional and structural insights into the unusual oxyanion hole... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kjj | ||||||
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Title | Functional and structural insights into the unusual oxyanion hole-like geometry in macrolactin acyltransferase selective for dicarboxylic acyl donors | ||||||
![]() | Putative beta-lactamase | ||||||
![]() | TRANSFERASE / acyltransferase | ||||||
Function / homology | Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / Chem-D9L / Putative beta-lactamase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xiao, F. / Dong, S. / Feng, Y. / Li, W. | ||||||
![]() | ![]() Title: Structural Basis of Specificity for Carboxyl-Terminated Acyl Donors in a Bacterial Acyltransferase. Authors: Xiao, F. / Dong, S. / Liu, Y. / Feng, Y. / Li, H. / Yun, C.H. / Cui, Q. / Li, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.4 KB | Display | ![]() |
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PDB format | ![]() | 126 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 677.2 KB | Display | ![]() |
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Full document | ![]() | 678.3 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kjhSC ![]() 6kjpC ![]() 6kjqC ![]() 6kjrC ![]() 6kjtC 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: 44223.426 Da / Num. of mol.: 1 / Mutation: S73A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-D9L / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.3, 25 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.49→117.99 Å / Num. obs: 13437 / % possible obs: 99.9 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.028 / Rrim(I) all: 0.102 / Net I/σ(I): 22.5 / Num. measured all: 184221 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6KJH Resolution: 2.492→39.165 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.2 Å2 / Biso mean: 37.4035 Å2 / Biso min: 10.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.492→39.165 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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