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Yorodumi- PDB-6e97: Crystal structure of the aryl acid adenylating enzyme FscC from F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6.0E+97 | ||||||
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Title | Crystal structure of the aryl acid adenylating enzyme FscC from Fuscachelin NRPS in complex with DHB-adenylate | ||||||
Components | 2,3-dihydroxybenzoate-AMP ligase | ||||||
Keywords | LIGASE / siderophore biosynthesis / adenylation domain / dihydroxybenzoic acid activating enzyme | ||||||
Function / homology | Function and homology information 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / siderophore biosynthetic process / ligase activity Similarity search - Function | ||||||
Biological species | Thermobifida fusca (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bruner, S.D. / Zagulyaeva, A.A. | ||||||
Citation | Journal: To Be Published Title: Implication of MbtH-like proteins in crystallization of the independent NRPS A domains. Crystal structure of FscC: supporting rationale for revised mechanism of freestanding aryl acid adenylating enzymes 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 | 6e97.cif.gz | 234.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e97.ent.gz | 182.8 KB | Display | PDB format |
PDBx/mmJSON format | 6e97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e97_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6e97_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6e97_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 6e97_validation.cif.gz | 63.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/6e97 ftp://data.pdbj.org/pub/pdb/validation_reports/e9/6e97 | HTTPS FTP |
-Related structure data
Related structure data | 6e8oC 1mdbS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 59746.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: Tfu_1871 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q47NR5 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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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: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG10000, lithium sulfate, Tris-HCl |
-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: Mar 21, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.8→50 Å / Num. obs: 93921 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.103 / Χ2: 2.221 / Net I/σ(I): 8.5 / Num. measured all: 674977 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MDB Resolution: 1.8→41.67 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.76 Å2 / Biso mean: 21.6121 Å2 / Biso min: 7.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→41.67 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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