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Yorodumi- PDB-3upo: Structure of penicillin-binding protein A from M. tuberculosis: p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3upo | ||||||
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Title | Structure of penicillin-binding protein A from M. tuberculosis: penicillin G acyl-enzyme complex | ||||||
Components | Penicillin-binding protein A | ||||||
Keywords | Penicillin-binding protein/Antibiotic / TRANSPEPTIDASE / peptidoglycan peptide / beta-lactam / Penicillin-binding protein-Antibiotic complex | ||||||
Function / homology | Function and homology information peptidoglycan L,D-transpeptidase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / membrane => GO:0016020 / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Davies, C. / Fedorovich, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: The role of the beta5-alpha11 loop in the active-site dynamics of acylated penicillin-binding protein A from Mycobacterium tuberculosis Authors: Fedarovich, A. / Nicholas, R.A. / Davies, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3upo.cif.gz | 327.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3upo.ent.gz | 268.2 KB | Display | PDB format |
PDBx/mmJSON format | 3upo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/3upo ftp://data.pdbj.org/pub/pdb/validation_reports/up/3upo | HTTPS FTP |
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-Related structure data
Related structure data | 3un7C 3upnC 3uppC 3lo7S 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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-Components
#1: Protein | Mass: 48464.492 Da / Num. of mol.: 2 / Fragment: UNP residues 35-491 / Mutation: G384R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT0019, MTCY10H4.16c, pbpA, Rv0016c / Plasmid: pT7HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P71586, UniProt: P9WKD1*PLUS, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | MUTATION IS PRESUMED TO HAVE BEEN INTRODUCED | |
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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: 2.2 Å3/Da / Density % sol: 44.07 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2009 |
Radiation | Monochromator: SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→44.3 Å / Num. all: 36564 / Num. obs: 36564 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 34 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.7 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3LO7 Resolution: 2.3→44.28 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 16.457 / SU ML: 0.187 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.249 / 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: 46.642 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→44.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.361 Å / Total num. of bins used: 20
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