+Open data
-Basic information
Entry | Database: PDB / ID: 6h27 | ||||||
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Title | Structure of S70C BlaC from Mycobacterium tuberculosis | ||||||
Components | BlaC | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Tassoni, R. / Pannu, N.S. / Ubbink, M. | ||||||
Citation | Journal: Biochemistry / Year: 2019 Title: New Conformations of Acylation Adducts of Inhibitors of beta-Lactamase from Mycobacterium tuberculosis. Authors: Tassoni, R. / Blok, A. / Pannu, N.S. / Ubbink, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h27.cif.gz | 115.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h27.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 6h27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h27_validation.pdf.gz | 460.3 KB | Display | wwPDB validaton report |
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Full document | 6h27_full_validation.pdf.gz | 465.5 KB | Display | |
Data in XML | 6h27_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 6h27_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/6h27 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/6h27 | HTTPS FTP |
-Related structure data
Related structure data | 6h28C 6h2aC 6h2cC 6h2gC 6h2hC 6h2iC 6h2kC 2gdnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 28 - 294 / Label seq-ID: 1 - 267
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-Components
#1: Protein | Mass: 29491.123 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A5I7 #2: Chemical | ChemComp-EDO / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.54 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NH4NO3 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→79.31 Å / Num. obs: 58936 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rpim(I) all: 0.05 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 6.7 % / Num. unique obs: 2940 / CC1/2: 0.762 / Rpim(I) all: 0.377 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GDN Resolution: 1.63→79.31 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.079 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.125 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.679 Å2
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Refinement step | Cycle: 1 / Resolution: 1.63→79.31 Å
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Refine LS restraints |
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