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Yorodumi- PDB-4u3t: Crystal structure of the transpeptidase domain of Neisseria gonor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u3t | ||||||
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Title | Crystal structure of the transpeptidase domain of Neisseria gonorrhoeae penicillin-binding protein 2 derived from the penicillin-resistant strain 6140 | ||||||
Components | Penicillin-binding protein 2 | ||||||
Keywords | HYDROLASE / penicillin-binding protein / transpeptidase domain / peptidoglycan synthesis / antibiotic resistance | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic ...peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Neisseria gonorrhoeae FA6140 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Fedarovich, A. / Davies, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2014 Title: Structural Effect of the Asp345a Insertion in Penicillin-Binding Protein 2 from Penicillin-Resistant Strains of Neisseria gonorrhoeae. Authors: Fedarovich, A. / Cook, E. / Tomberg, J. / 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 | 4u3t.cif.gz | 248.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u3t.ent.gz | 199 KB | Display | PDB format |
PDBx/mmJSON format | 4u3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u3t_validation.pdf.gz | 439.9 KB | Display | wwPDB validaton report |
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Full document | 4u3t_full_validation.pdf.gz | 446.1 KB | Display | |
Data in XML | 4u3t_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 4u3t_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/4u3t ftp://data.pdbj.org/pub/pdb/validation_reports/u3/4u3t | HTTPS FTP |
-Related structure data
Related structure data | 3equS S: Starting model for refinement |
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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: 35411.320 Da / Num. of mol.: 2 / Fragment: transpeptidase domain (UNP residues 237-574) / Mutation: D346a, F504L, A510V, A516G, P551S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae FA6140 (bacteria) Gene: penA / Plasmid: pMAL-C2KV / Production host: Escherichia coli (E. coli) / Strain (production host): GW6011 References: UniProt: P08149, 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: 2.16 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 21% PEG 6000, 0.1 M HEPES pH 7.8 / PH range: 7.8 |
-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: Jul 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 29597 / Num. obs: 29597 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 4.2 / % possible all: 78 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3EQU Resolution: 2.2→35.45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.348 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 42.1 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→35.45 Å
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