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Yorodumi- PDB-6p63: Wild-type NIS synthetase DesD bound to AMP and substrate analog c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p63 | |||||||||
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Title | Wild-type NIS synthetase DesD bound to AMP and substrate analog cadaverine | |||||||||
Components | Siderophore Synthetase Type C DesD | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / NIS synthetase / siderophore synthesis | |||||||||
Function / homology | Function and homology information acid-amino acid ligase activity / siderophore biosynthetic process / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Streptomyces coelicolor (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Hoffmann, K.M. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2020 Title: Cofactor Complexes of DesD, a Model Enzyme in the Virulence-related NIS Synthetase Family. Authors: Hoffmann, K.M. / Goncuian, E.S. / Karimi, K.L. / Amendola, C.R. / Mojab, Y. / Wood, K.M. / Prussia, G.A. / Nix, J. / Yamamoto, M. / Lathan, K. / Orion, I.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p63.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6p63.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 6p63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/6p63 ftp://data.pdbj.org/pub/pdb/validation_reports/p6/6p63 | HTTPS FTP |
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-Related structure data
Related structure data | 6xrcC 2x0oS 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
#1: Protein | Mass: 66665.211 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: CAB87222 / Plasmid: pET44b / Details (production host): C-terminal hexa his tag / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L069 #2: Chemical | ChemComp-AMP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.51 Å3/Da / Density % sol: 50.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.16 M magnesium chloride, 20% PEG, 0.08 M Tris hexahydrate, pH 8.5, 15% glycerol, 10% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: cryo-cooled / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 16, 2014 / Details: varimax DW |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→89.53 Å / Num. obs: 99262 / % possible obs: 96.2 % / Redundancy: 3.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.081 / Rrim(I) all: 0.121 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4758 / CC1/2: 0.841 / Rpim(I) all: 0.296 / Rrim(I) all: 0.456 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2X0O Resolution: 2.4→69.832 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.164 / Average fsc free: 0.9242 / Average fsc work: 0.9404 / Cross valid method: THROUGHOUT / ESU R: 0.481 / ESU R Free: 0.258 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.251 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→69.832 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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