+Open data
-Basic information
Entry | Database: PDB / ID: 6e1q | ||||||
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Title | AtGH3.15 acyl acid amido synthetase in complex with 2,4-DB | ||||||
Components | AtGH3.15 acyl acid amido synthetase | ||||||
Keywords | LIGASE / hormone modification / adenylating enzyme / acyl acid-amido synthetase / adenylation / plant protein | ||||||
Function / homology | Function and homology information auxin conjugate metabolic process / glutamine binding / acid-amino acid ligase activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.148 Å | ||||||
Authors | Sharp, A.M. / Lee, S.G. / Jez, J.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Modification of auxinic phenoxyalkanoic acid herbicides by the acyl acid amido synthetase GH3.15 from Arabidopsis. Authors: Sherp, A.M. / Lee, S.G. / Schraft, E. / Jez, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e1q.cif.gz | 249.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e1q.ent.gz | 200 KB | Display | PDB format |
PDBx/mmJSON format | 6e1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e1q_validation.pdf.gz | 456 KB | Display | wwPDB validaton report |
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Full document | 6e1q_full_validation.pdf.gz | 463.6 KB | Display | |
Data in XML | 6e1q_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 6e1q_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/6e1q ftp://data.pdbj.org/pub/pdb/validation_reports/e1/6e1q | HTTPS FTP |
-Related structure data
Related structure data | 6avhS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 67052.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g13370, At5g13370/T22N19_20, T22N19.20, T22N19_20 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8GZ29, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||
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#2: Chemical | ChemComp-PO4 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1.2 M potassium phosphate dibasic, 0.8 M sodium phosphate monobasic, 0.1 M sodium acetate/acetic acid, 2.5 mM 2,4-DB |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.148→38.7 Å / Num. obs: 47900 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rsym value: 0.047 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.148→2.19 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.557 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6AVH Resolution: 2.148→38.697 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.02 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.148→38.697 Å
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Refine LS restraints |
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LS refinement shell |
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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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