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Open data
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Basic information
Entry | Database: PDB / ID: 7dxm | ||||||
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Title | Crystal structure of DltD | ||||||
![]() | Protein DltD | ||||||
![]() | TRANSFERASE / O-acyltransferase / dlt operon | ||||||
Function / homology | DltD / D-alanyl-lipoteichoic acid biosynthesis DltD, Firmicutes / DltD protein / lipoteichoic acid biosynthetic process / membrane => GO:0016020 / plasma membrane / Protein DltD![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yan, X.X. / Zeng, Q. / Tian, L.F. | ||||||
![]() | ![]() Title: Crystal Structure of an O-acyltransfer Terminal Protein stDltD and Its Implications for dlt Operon-mediated D-alanylation of S. thermophilus. Authors: Zeng, Q. / Tian, L.F. / Liu, Y.P. / Yan, X.X. / Xu, W.Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 316.4 KB | Display | ![]() |
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PDB format | ![]() | 259.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 56.8 KB | Display | |
Data in CIF | ![]() | 77.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bmaS 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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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45829.043 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LMG 18311 / Gene: dltD / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density meas: 53.22 Mg/m3 / Density % sol: 50.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% glycerol, 14% [w/v] PEG6000, 170 mM (NH4)2SO4) |
-Data collection
Diffraction | Mean temperature: 81 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.96→40 Å / Num. obs: 38815 / % possible obs: 99.2 % / Redundancy: 4 % / CC1/2: 0.984 / Rpim(I) all: 0.105 / Rrim(I) all: 0.215 / Net I/σ(I): 10.85 |
Reflection shell | Resolution: 2.96→3.01 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1904 / CC1/2: 0.554 / Rpim(I) all: 0.573 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3BMA Resolution: 2.96→40 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.96→40 Å
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