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- PDB-7ajo: The X-ray Structure of L,D-transpeptidase LdtA from Vibrio choler... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ajo | ||||||
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Title | The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with the cross-linking reaction intermediate | ||||||
![]() | 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 in complex with the cross-linking reaction intermediate 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 | ![]() | 128.6 KB | Display | ![]() |
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PDB format | ![]() | 95.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 780.9 KB | Display | ![]() |
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Full document | ![]() | 784.2 KB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 37.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7aj9S 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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Unit cell |
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Components
#1: Protein | Mass: 60418.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-S2K / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion 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: Jul 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→46.67 Å / Num. obs: 58138 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.997 / Rpim(I) all: 0.069 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 6.4 / Num. unique obs: 3549 / CC1/2: 0.409 / Rpim(I) all: 1.042 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7AJ9 Resolution: 1.85→46.67 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.995 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 121.67 Å2 / Biso mean: 30.197 Å2 / Biso min: 15.11 Å2
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Refinement step | Cycle: final / Resolution: 1.85→46.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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