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Yorodumi- PDB-7ajx: The X-ray Structure of L,D-transpeptidase LdtA from Vibrio choler... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ajx | ||||||
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Title | The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with meropenem | ||||||
Components | L,D-transpeptidase YcbB | ||||||
Keywords | TRANSFERASE / L / D-transpeptidase | ||||||
Function / homology | Function and homology information peptidoglycan biosynthetic process / carboxypeptidase activity / transferase activity Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Batuecas, M.T. / Hermoso, J.A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: To Be Published Title: The X-ray Structure of L,D-transpeptidase LdtA from Vibrio cholerae in complex with meropenem Authors: Batuecas, M.T. / Hermoso, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ajx.cif.gz | 121.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ajx.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ajx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ajx_validation.pdf.gz | 715.8 KB | Display | wwPDB validaton report |
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Full document | 7ajx_full_validation.pdf.gz | 720.4 KB | Display | |
Data in XML | 7ajx_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 7ajx_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/7ajx ftp://data.pdbj.org/pub/pdb/validation_reports/aj/7ajx | HTTPS FTP |
-Related structure data
Related structure data | 7aj9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Vibrio cholerae (bacteria) / Gene: ERS013138_01558, ERS013186_00077, ERS013206_00149 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A655UKB5 |
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#2: Chemical | ChemComp-MXR / ( Mass: 385.478 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Formula: C17H27N3O5S / Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ERS013138_01558, ERS013186_00077, ERS013206_00149 / Production host: Escherichia coli BL21(DE3) (bacteria) / Feature type: SUBJECT OF INVESTIGATION |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion Details: 0.1M 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: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97916 Å |
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: 2.55→46.386 Å / Num. obs: 22790 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rpim(I) all: 0.068 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.55→2.66 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2750 / CC1/2: 0.516 / Rpim(I) all: 1.038 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AJ9 Resolution: 2.55→46.34 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 16.229 / SU ML: 0.316 / Cross valid method: FREE R-VALUE / ESU R: 0.473 / ESU R Free: 0.3 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.039 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→46.34 Å
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Refine LS restraints |
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LS refinement shell |
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