+Open data
-Basic information
Entry | Database: PDB / ID: 8da2 | ||||||
---|---|---|---|---|---|---|---|
Title | Acinetobacter baumannii L,D-transpeptidase | ||||||
Components | L,D-transpeptidase family protein | ||||||
Keywords | TRANSFERASE / cell wall / transpeptidase / peptidoglycan | ||||||
Function / homology | Function and homology information peptidoglycan L,D-transpeptidase activity / peptidoglycan biosynthetic process / transferase activity Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Toth, M. / Stewart, N.K. / Smith, C.A. / Vakulenko, S.B. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Acs Infect Dis. / Year: 2022 Title: The l,d-Transpeptidase Ldt Ab from Acinetobacter baumannii Is Poorly Inhibited by Carbapenems and Has a Unique Structural Architecture. Authors: Toth, M. / Stewart, N.K. / Smith, C.A. / Lee, M. / Vakulenko, S.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8da2.cif.gz | 137.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8da2.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 8da2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/8da2 ftp://data.pdbj.org/pub/pdb/validation_reports/da/8da2 | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 42314.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: ABR2091_2609, F4T85_00805, GSE42_14305, H0529_01000, HBK86_12775 Production host: Escherichia coli (E. coli) / References: UniProt: A0A222A2P4 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium formate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→37.1 Å / Num. obs: 16048 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rpim(I) all: 0.041 / Rrim(I) all: 0.111 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.6→2.72 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1910 / CC1/2: 0.932 / Rpim(I) all: 0.42 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.6→37.06 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 36.86 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 143.14 Å2 / Biso mean: 74.4764 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→37.06 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|