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Open data
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Basic information
Entry | Database: PDB / ID: 7dnp | ||||||
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Title | Structure of Brucella abortus SagA | ||||||
![]() | Secretion activator protein, hypothetical | ||||||
![]() | HYDROLASE / SagA / muramidase / brucella abortus / T4SS | ||||||
Function / homology | TtsA-like, Glycoside hydrolase family 108 domain / Peptidoglycan binding domain / Glycosyl hydrolase 108 / Predicted Peptidoglycan domain / Lysozyme-like domain superfamily / membrane => GO:0016020 / Chem-H9U / Secretion activator protein, hypothetical![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hyun, Y. / Ha, N.-C. | ||||||
![]() | ![]() Title: Structure and Function of the Autolysin SagA in the Type IV Secretion System of Brucella abortus . Authors: Hyun, Y. / Baek, Y. / Lee, C. / Ki, N. / Ahn, J. / Ryu, S. / Ha, N.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 | ![]() | 58.8 KB | Display | ![]() |
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PDB format | ![]() | 33.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 19780.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 9-941 / Gene: BruAb1_0990 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-H9U / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.87 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate (pH 4.1), 21% (w/v) polyethylene glycol 4,000, 2 mM Tris(2-chloroethyl) phosphate (TCEP) |
-Data collection
Diffraction | Mean temperature: 100.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 11424 / % possible obs: 100 % / Redundancy: 30.7 % / Biso Wilson estimate: 23.35 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.009 / Rrim(I) all: 0.056 / Net I/σ(I): 67.5 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 15.6 / Num. unique obs: 570 / CC1/2: 0.989 / CC star: 0.997 / Rpim(I) all: 0.043 / Rrim(I) all: 0.219 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.44 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→45.63 Å
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Refine LS restraints |
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LS refinement shell |
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