+Open data
-Basic information
Entry | Database: PDB / ID: 5g4a | |||||||||
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Title | AadA in complex with ATP and magnesium | |||||||||
Components | (Aminoglycoside (3'') (9) ...) x 2 | |||||||||
Keywords | TRANSFERASE / AMINOGLYCOSIDE ADENYL TRANSFERASE / ANT(3'')9 / ANTIBIOTIC RESISTANCE | |||||||||
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 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Stern, A.L. / van der Verren, S. / Selmer, M. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2018 Title: Structural mechanism of AadA, a dual-specificity aminoglycoside adenylyltransferase fromSalmonella enterica. Authors: Stern, A.L. / Van der Verren, S.E. / Kanchugal P, S. / Nasvall, J. / Gutierrez-de-Teran, H. / Selmer, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g4a.cif.gz | 257.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g4a.ent.gz | 205.7 KB | Display | PDB format |
PDBx/mmJSON format | 5g4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g4a_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5g4a_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5g4a_validation.xml.gz | 27 KB | Display | |
Data in CIF | 5g4a_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/5g4a ftp://data.pdbj.org/pub/pdb/validation_reports/g4/5g4a | HTTPS FTP |
-Related structure data
Related structure data | 5lpaC 5luhC 6fzbC 4cs6S 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
-Aminoglycoside (3'') (9) ... , 2 types, 2 molecules AB
#1: Protein | Mass: 30604.154 Da / Num. of mol.: 1 Fragment: NUCLEOTIDYLTRANSFERASE DOMAIN AND ALPHA-HELICAL DOMAIN Source method: isolated from a genetically manipulated source Details: C-TERMINAL HEXAHISTIDINE TAG / Source: (gene. exp.) Salmonella enterica (bacteria) / Strain: ENTERICA SEROVAR TYPHIMURIUM STR. LT2 / Gene: aadA / Plasmid: PEXP5-CT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0W4NPT0, UniProt: Q8ZPX9*PLUS |
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#2: Protein | Mass: 30572.088 Da / Num. of mol.: 1 Fragment: NUCLEOTIDYLTRANSFERASE DOMAIN AND ALPHA-HELICAL DOMAIN Source method: isolated from a genetically manipulated source Details: C-TERMINAL HEXAHISTIDINE TAG / Source: (gene. exp.) Salmonella enterica (bacteria) / Strain: ENTERICA SEROVAR TYPHIMURIUM STR. LT2 / Gene: aadA / Plasmid: PEXP5-CT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0W4NPT0, UniProt: Q8ZPX9*PLUS |
-Non-polymers , 8 types, 553 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Chemical | ChemComp-UNX / #9: Chemical | ChemComp-PGE / | #10: Water | ChemComp-HOH / | |
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-Details
Sequence details | SEQUENCE |
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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: 2.55 Å3/Da / Density % sol: 51.8 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 10% W/V PEG 20 000, 20% V/V PEG MME 550, 0.1 M BICINE/TRIZMA BASE PH 8.5, 0.02 M EACH OF SODIUM L-GLUTAMATE, DL-ALANINE, GLYCINE, DL-LYSINE HCL AND DL-SERINE (MORPHEUS SCREEN, MOLECULAR DIMENSIONS) |
-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: Apr 28, 2014 / Details: PT COATED MIRRORS |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.165 Å / Num. obs: 46215 / % possible obs: 96.9 % / Observed criterion σ(I): -0.3 / Redundancy: 9.7 % / Biso Wilson estimate: 23.21 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.52 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CS6 Resolution: 1.9→41.165 Å / SU ML: 0.26 / σ(F): 2.39 / Phase error: 25.11 / Stereochemistry target values: ML Details: THERE IS WEAK UN-MODELLED DENSITY FOR THE C-TERMINAL HEXAHISTIDINE TAG. WATER MOLECULES A2130, A2131, A2044 AND B2032, B2101, B2102 ARE MODELLED IN DENSITY THAT MAY REPRESENT AN UNKNOWN LIGAND.
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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: 32.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→41.165 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: -12.9525 Å / Origin y: 71.339 Å / Origin z: 56.9177 Å
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Refinement TLS group | Selection details: ALL |