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Yorodumi- PDB-6ea3: Thermobifida fusca FscH adenylation domain complexed with MbtH-li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ea3 | ||||||
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Title | Thermobifida fusca FscH adenylation domain complexed with MbtH-like protein FscK and Ser-AMP | ||||||
Components |
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Keywords | LIGASE / siderophore biosynthesis / serine activating adenylation domain / MbtH-like protein / seryl-adenylate | ||||||
Function / homology | Function and homology information small molecule metabolic process / amide biosynthetic process / organonitrogen compound biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / catalytic activity Similarity search - Function | ||||||
Biological species | Thermobifida fusca (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Bruner, S.D. / Zagulyaeva, A.A. | ||||||
Citation | Journal: To Be Published Title: Comprehensive analysis of protein-protein interactions between MbtH-like protein FscK and adenylation domains in nonribosomal biosynthesis of Fuscachelins. Authors: Bruner, S.D. / Zagulyaeva, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ea3.cif.gz | 122.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ea3.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 6ea3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/6ea3 ftp://data.pdbj.org/pub/pdb/validation_reports/ea/6ea3 | HTTPS FTP |
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-Related structure data
Related structure data | 6ebyC 4gr4S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9094.947 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria) Strain: YX / Gene: Tfu_1863 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47NS3 |
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#2: Protein | Mass: 59241.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida fusca (strain YX) (bacteria) Strain: YX / Gene: Tfu_1866 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47NS0 |
#3: Chemical | ChemComp-SRP / |
#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: 2.34 Å3/Da / Density % sol: 47.47 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, sodium chloride, BisTris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 16, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→27.827 Å / Num. obs: 143171 / % possible obs: 96.8 % / Redundancy: 3.181 % / Biso Wilson estimate: 17.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.056 / Χ2: 1.03 / Net I/σ(I): 14.37 / Num. measured all: 455412 / Scaling rejects: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GR4 Resolution: 1.65→27.827 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.2 Å2 / Biso mean: 23.0606 Å2 / Biso min: 10.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→27.827 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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