+Open data
-Basic information
Entry | Database: PDB / ID: 6akd | ||||||
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Title | Crystal structure of IdnL7 | ||||||
Components | AMP-dependent synthetase and ligase | ||||||
Keywords | LIGASE / ATP-binding / five layered alpha-beta-alpha-beta-alpha sandwich fold | ||||||
Function / homology | ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / ligase activity / '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE / AMP-dependent synthetase and ligase Function and homology information | ||||||
Biological species | Streptomyces sp. ML694-90F3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cieslak, J. / Miyanaga, A. / Kudo, F. / Eguchi, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2019 Title: Functional and structural characterization of IdnL7, an adenylation enzyme involved in incednine biosynthesis. Authors: Cieslak, J. / Miyanaga, A. / Takaishi, M. / Kudo, F. / Eguchi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6akd.cif.gz | 204 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6akd.ent.gz | 159.8 KB | Display | PDB format |
PDBx/mmJSON format | 6akd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6akd_validation.pdf.gz | 828.9 KB | Display | wwPDB validaton report |
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Full document | 6akd_full_validation.pdf.gz | 832.8 KB | Display | |
Data in XML | 6akd_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 6akd_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/6akd ftp://data.pdbj.org/pub/pdb/validation_reports/ak/6akd | HTTPS FTP |
-Related structure data
Related structure data | 1amuS 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
#1: Protein | Mass: 57514.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. ML694-90F3 (bacteria) / Strain: ML694-90F / Gene: idnL7 / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: A0A077KUW8 | ||
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#2: Chemical | ChemComp-A5A / ' | ||
#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: 2.3 Å3/Da / Density % sol: 46.48 % |
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Crystal grow | Temperature: 299 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Tris, 0.2M magnesium chloride, 30% PEG4000, 0.5mM [N-(L-alanyl)sulfamoyl] adenosine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 2, 2015 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 32390 / % possible obs: 99.7 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 33.4 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1587 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AMU Resolution: 2.1→43.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.933 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.168 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.169 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→43.54 Å
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Refine LS restraints |
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