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Yorodumi- PDB-7tgk: Crystal structure of ATP bound DesD, the desferrioxamine syntheta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tgk | |||||||||
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Title | Crystal structure of ATP bound DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway | |||||||||
Components | Desferrioxamine synthetase DesD | |||||||||
Keywords | LIGASE / NRPS-independent siderophore (NIS) synthetase / iterative synthetase / amide ligase / adenylate-forming enzyme | |||||||||
Function / homology | ADENOSINE-5'-TRIPHOSPHATE Function and homology information | |||||||||
Biological species | Streptomyces griseoflavus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Patel, K.D. / Gulick, A.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD. Authors: Yang, J. / Banas, V.S. / Patel, K.D. / Rivera, G.S.M. / Mydy, L.S. / Gulick, A.M. / Wencewicz, T.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tgk.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7tgk.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 7tgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tgk_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 7tgk_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 7tgk_validation.xml.gz | 110.6 KB | Display | |
Data in CIF | 7tgk_validation.cif.gz | 153.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/7tgk ftp://data.pdbj.org/pub/pdb/validation_reports/tg/7tgk | HTTPS FTP |
-Related structure data
Related structure data | 7tgjSC 7tglC 7tgmC 7tgnC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
-Protein , 1 types, 5 molecules DBEAC
#1: Protein | Mass: 68761.516 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) |
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-Non-polymers , 6 types, 872 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | ChemComp-MPD / ( #7: Water | ChemComp-HOH / | |
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-Details
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: 3.57 Å3/Da / Density % sol: 65.53 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.05M BTP pH 7.0, 0.2M Ammonium sulfate 16% PEG 4000 (under oil 100%) |
-Data collection
Diffraction | Mean temperature: 113 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49 Å / Num. obs: 216739 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 50.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.04 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.3→2.42 Å / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 250917 / CC1/2: 0.627 / Rpim(I) all: 0.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: unliganded FerDesD 7TGJ Resolution: 2.3→48.95 Å / SU ML: 0.2793 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.602 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 55.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→48.95 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 82.3981125971 Å / Origin y: 45.3697109472 Å / Origin z: -42.9354161498 Å
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Refinement TLS group | Selection details: all |