+Open data
-Basic information
Entry | Database: PDB / ID: 3lo7 | ||||||
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Title | Crystal structure of PBPA from Mycobacterium tuberculosis | ||||||
Components | Penicillin-binding protein A | ||||||
Keywords | TRANSFERASE / TRANSPEPTIDASE DOMAIN / Cell membrane / Cell shape / Cell wall biogenesis/degradation / Membrane / Peptidoglycan synthesis / Phosphoprotein / Signal-anchor / Transmembrane | ||||||
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 / MAD / Resolution: 2.05 Å | ||||||
Authors | Fedarovich, A. / Davies, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Unusual conformation of the SxN motif in the crystal structure of 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 | 3lo7.cif.gz | 302.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lo7.ent.gz | 255.5 KB | Display | PDB format |
PDBx/mmJSON format | 3lo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lo7_validation.pdf.gz | 449.4 KB | Display | wwPDB validaton report |
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Full document | 3lo7_full_validation.pdf.gz | 460.2 KB | Display | |
Data in XML | 3lo7_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 3lo7_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/3lo7 ftp://data.pdbj.org/pub/pdb/validation_reports/lo/3lo7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 51150.332 Da / Num. of mol.: 2 / Fragment: UNP residues 35 to 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: 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: 1.89 Å3/Da / Density % sol: 34.99 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 35% PEG 1000, 0.2M ammonium acetate, 0.1 M sodium acetate, pH 4.6, 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: 0.97932,0.97946,0.97180 | ||||||||||||
Detector | Type: MAR CCD 225 mm / Detector: CCD / Date: Jun 27, 2005 | ||||||||||||
Radiation | Monochromator: SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.05→36.3 Å / Num. all: 47630 / Num. obs: 47630 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 45.9 | ||||||||||||
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4701 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.05→36.3 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 11.457 / SU ML: 0.15 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 44.796 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→36.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.051→2.104 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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