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Yorodumi- PDB-5crf: Structure of the penicillin-binding protein PonA1 from Mycobacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5crf | ||||||
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Title | Structure of the penicillin-binding protein PonA1 from Mycobacterium Tuberculosis | ||||||
Components | Penicillin-binding protein 1A | ||||||
Keywords | PENICILLIN-BINDING PROTEIN / b-lactam / PBP / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI | ||||||
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 / SAD / Resolution: 1.8 Å | ||||||
Authors | Filippova, E.V. / Wawrzak, Z. / 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 | 5crf.cif.gz | 582.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5crf.ent.gz | 496.6 KB | Display | PDB format |
PDBx/mmJSON format | 5crf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/5crf ftp://data.pdbj.org/pub/pdb/validation_reports/cr/5crf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 44637.605 Da / Num. of mol.: 4 / 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 #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | Sequence details | The protein degraded during crystallization experiments. The C-terminal transpeptidase domain was ...The protein degraded during crystallization experiments. The C-terminal transpeptidase domain was crystallized and obtained in the crystal structure. | |
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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: 1.81 Å3/Da / Density % sol: 31.91 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Lithium chloride, 0.1 M HEPES, 20 % PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 17, 2014 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987857 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 120754 / % possible obs: 96.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.4 / % possible all: 97.6 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.084 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.124 / 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: 31.899 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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