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- PDB-7aj9: The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae -
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Open data
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Basic information
Entry | Database: PDB / ID: 7aj9 | ||||||
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Title | The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae | ||||||
![]() | L,D-transpeptidase YcbB | ||||||
![]() | TRANSFERASE / L / D-transpeptidase | ||||||
Function / homology | ![]() peptidoglycan biosynthetic process / carboxypeptidase activity / transferase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Batuecas, M.T. / Hermoso, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae Authors: Batuecas, M.T. / Hermoso, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.4 KB | Display | ![]() |
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PDB format | ![]() | 169.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1007.1 KB | Display | ![]() |
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Full document | ![]() | 1020.1 KB | Display | |
Data in XML | ![]() | 35.2 KB | Display | |
Data in CIF | ![]() | 48.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 60418.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #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: 2.84 Å3/Da / Density % sol: 56.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES pH 7 + 10% PEG 8000 + 10% Ethylene Glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97927 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→47.34 Å / Num. obs: 54368 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rpim(I) all: 0.057 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.35→2.42 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4391 / CC1/2: 0.411 / Rpim(I) all: 1.279 / % possible all: 99.9 |
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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 : REFINED INDIVIDUALLY
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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: 200.3 Å2 / Biso mean: 67.837 Å2 / Biso min: 28.12 Å2
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Refinement step | Cycle: final / Resolution: 2.35→47.34 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 14580 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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