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Yorodumi- PDB-6h2a: Structure of S70A BlaC from Mycobacterium tuberculosis obtained f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h2a | ||||||
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Title | Structure of S70A BlaC from Mycobacterium tuberculosis obtained from crystals produced in the presence of DTT | ||||||
Components |
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Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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 | 6h2a.cif.gz | 161.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h2a.ent.gz | 127.2 KB | Display | PDB format |
PDBx/mmJSON format | 6h2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h2a_validation.pdf.gz | 512.9 KB | Display | wwPDB validaton report |
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Full document | 6h2a_full_validation.pdf.gz | 524.7 KB | Display | |
Data in XML | 6h2a_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 6h2a_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/6h2a ftp://data.pdbj.org/pub/pdb/validation_reports/h2/6h2a | HTTPS FTP |
-Related structure data
Related structure data | 6h27C 6h28C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: _
NCS ensembles :
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCH
#1: Protein | Mass: 29459.061 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, ERS027646_02769 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0T9EA39, UniProt: A0A655AHQ9*PLUS, beta-lactamase #2: Protein/peptide | | Mass: 360.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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-Non-polymers , 5 types, 69 molecules
#3: Chemical | #4: Chemical | ChemComp-DTT / #5: Chemical | ChemComp-PO4 / #6: Chemical | ChemComp-GOL / #7: 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: 4.35 Å3/Da / Density % sol: 71.73 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl, pH 7.0 1.7 M NH4H2PO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→49.73 Å / Num. obs: 714649 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rpim(I) all: 0.034 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.54→2.63 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 71706 / CC1/2: 0.701 / Rpim(I) all: 0.49 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GDN Resolution: 2.54→49.73 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.371 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.231 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.052 Å2
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Refinement step | Cycle: 1 / Resolution: 2.54→49.73 Å
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Refine LS restraints |
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