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Yorodumi- PDB-3upp: Structure of penicillin-binding protein A from M. tuberculosis: c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3upp | |||||||||
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Title | Structure of penicillin-binding protein A from M. tuberculosis: ceftrixaone acyl-enzyme complex | |||||||||
Components | Penicillin-binding protein A | |||||||||
Keywords | Penicillin-binding protein/Antibiotic / TRANSPEPTIDASE / peptidoglycan / 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: 2.4 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 | 3upp.cif.gz | 329.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3upp.ent.gz | 270.1 KB | Display | PDB format |
PDBx/mmJSON format | 3upp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3upp_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3upp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3upp_validation.xml.gz | 32 KB | Display | |
Data in CIF | 3upp_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/3upp ftp://data.pdbj.org/pub/pdb/validation_reports/up/3upp | HTTPS FTP |
-Related structure data
Related structure data | 3un7C 3upnC 3upoC 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 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 / | Nonpolymer details | THE STARTING ANTIBIOTIC | Sequence details | THE MUTATION G384R OCCURED DURING PCR | |
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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: 2.29 Å3/Da / Density % sol: 46.19 % |
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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: Jun 12, 2011 |
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: 2.4→45.7 Å / Num. all: 33749 / Num. obs: 33749 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 34.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.2 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3LO7 Resolution: 2.4→40.29 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 20.76 / SU ML: 0.223 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.531 / ESU R Free: 0.275 / 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: 52.992 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→40.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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