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Yorodumi- PDB-5cxw: Structure of the PonA1 protein from Mycobacterium Tuberculosis in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cxw | ||||||
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Title | Structure of the PonA1 protein from Mycobacterium Tuberculosis in complex with penicillin V | ||||||
Components | Penicillin-binding protein 1A | ||||||
Keywords | PENICILLIN-BINDING PROTEIN/ANTIBIOTIC / b-lactam / PBP / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / PENICILLIN-BINDING PROTEIN-ANTIBIOTIC complex | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / outer membrane-bounded periplasmic space / regulation of cell shape / cellular response to hypoxia ...peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / outer membrane-bounded periplasmic space / regulation of cell shape / cellular response to hypoxia / response to antibiotic / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Filippova, E.V. / Kiryukhina, O. / Kieser, K. / Endres, M. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI) | ||||||
Citation | Journal: Febs J. / Year: 2016 Title: Crystal structures of the transpeptidase domain of the Mycobacterium tuberculosis penicillin-binding protein PonA1 reveal potential mechanisms of antibiotic resistance. Authors: Filippova, E.V. / Kieser, K.J. / Luan, C.H. / Wawrzak, Z. / Kiryukhina, O. / Rubin, E.J. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cxw.cif.gz | 168.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cxw.ent.gz | 128.6 KB | Display | PDB format |
PDBx/mmJSON format | 5cxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/5cxw ftp://data.pdbj.org/pub/pdb/validation_reports/cx/5cxw | HTTPS FTP |
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-Related structure data
Related structure data | 5crfSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44309.348 Da / Num. of mol.: 1 / Fragment: UNP residues 391-820 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: ponA1, Rv0050, MTCY21D4.13 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: P71707 | ||
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#2: Chemical | ChemComp-EPE / | ||
#3: Chemical | ChemComp-35P / ( | ||
#4: Chemical | #5: 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: 2.17 Å3/Da / Density % sol: 43.23 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 39656 / % possible obs: 99.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 3.1 / % possible all: 99 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CRF Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.774 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.1 / 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: 20.069 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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