+Open data
-Basic information
Entry | Database: PDB / ID: 4cs6 | ||||||
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Title | Crystal structure of AadA - an aminoglycoside adenyltransferase | ||||||
Components | AMINOGLYCOSIDE ADENYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / AMINOGLYCOSIDE ADENYLTRANSFERASE / ANT(3'') | ||||||
Function / homology | Function and homology information streptomycin 3''-adenylyltransferase / aminoglycoside 3''-adenylyltransferase activity / adenylyltransferase activity / response to antibiotic / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.502 Å | ||||||
Authors | Chen, Y. / Nasvall, J. / Andersson, D.I. / Selmer, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structure of Aada from Salmonella Enterica: A Monomeric Aminoglycoside (3'')(9) Adenyltransferase. Authors: Chen, Y. / Nasvall, J. / Wu, S. / Andersson, D.I. / Selmer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cs6.cif.gz | 112.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cs6.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cs6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cs6_validation.pdf.gz | 425.8 KB | Display | wwPDB validaton report |
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Full document | 4cs6_full_validation.pdf.gz | 428.9 KB | Display | |
Data in XML | 4cs6_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 4cs6_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/4cs6 ftp://data.pdbj.org/pub/pdb/validation_reports/cs/4cs6 | 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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Unit cell |
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-Components
#1: Protein | Mass: 29590.986 Da / Num. of mol.: 1 Fragment: NUCLEOTIDYLTRANSFERASE DOMAIN AND ALPHA-HELICAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2 (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q8ZPX9 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.21 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 193 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0, 0.9793 | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2013 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→39 Å / Num. obs: 10853 / % possible obs: 99.7 % / Observed criterion σ(I): 2.1 / Redundancy: 7.05 % / Biso Wilson estimate: 61.76 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17 | |||||||||
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 7.14 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.1 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.502→39.029 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 29.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.3 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.502→39.029 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 5.0012 Å / Origin y: 15.7438 Å / Origin z: 128.4074 Å
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Refinement TLS group | Selection details: ALL |