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Yorodumi- PDB-4df6: Crystal Structure of the inhibitor NXL104 Covalent Adduct with TB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4df6 | ||||||
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Title | Crystal Structure of the inhibitor NXL104 Covalent Adduct with TB B-lactamase | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / penicillin binding protein / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information penicillinase activity / cephalosporinase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Hazra, S. / Blanchard, J. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: NXL104 irreversibly inhibits the {beta}-lactamase from Mycobacterium tuberculosis. Authors: Xu, H. / Hazra, S. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4df6.cif.gz | 111.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4df6.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 4df6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/4df6 ftp://data.pdbj.org/pub/pdb/validation_reports/df/4df6 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: 28272.721 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaA, blaC, MT2128, MTCY49.07c, Rv2068c / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase | ||||
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#2: Chemical | #3: Chemical | ChemComp-NXL / ( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.92 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.1 Details: 0.1 M HEPES, 2 M ammonium phosphate monobasic, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→40.262 Å / Num. all: 11647 / Num. obs: 11647 / % possible obs: 96.2 % |
Reflection shell | Highest resolution: 2.29 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→40.26 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.895 / SU B: 15.688 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.652 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→40.26 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1982 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0 Å
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LS refinement shell | Resolution: 2.29→2.35 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -7.2843 Å / Origin y: -6.9233 Å / Origin z: -8.6345 Å
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