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Yorodumi- PDB-4u0o: Crystal structure of Thermosynechococcus elongatus Lipoyl Synthas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u0o | |||||||||
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Title | Crystal structure of Thermosynechococcus elongatus Lipoyl Synthase 2 complexed with MTA and DTT | |||||||||
Components | Lipoyl synthase 2 | |||||||||
Keywords | TRANSFERASE / radical SAM / TIM barrel / sulfotransferase | |||||||||
Function / homology | Function and homology information lipoyl synthase / lipoate synthase activity / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermosynechococcus elongatus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | |||||||||
Authors | Harmer, J.E. / Hiscox, M.J. / Dinis, P.C. / Sandy, J. / Roach, P.L. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biochem.J. / Year: 2014 Title: Structures of lipoyl synthase reveal a compact active site for controlling sequential sulfur insertion reactions. Authors: Harmer, J.E. / Hiscox, M.J. / Dinis, P.C. / Fox, S.J. / Iliopoulos, A. / Hussey, J.E. / Sandy, J. / Van Beek, F.T. / Essex, J.W. / Roach, P.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u0o.cif.gz | 118.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u0o.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 4u0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/4u0o ftp://data.pdbj.org/pub/pdb/validation_reports/u0/4u0o | HTTPS FTP |
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-Related structure data
Related structure data | 4u0pSC 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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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 32605.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (bacteria) Strain: BP-1 / Gene: lipA2, tll0574 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DLC2, lipoyl synthase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-DTT / | #4: Chemical | ChemComp-MTA / | #5: 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: 2.74 Å3/Da / Density % sol: 55.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM bicine pH 8.5, 15% PEG 20,000, 3% dextran sulfate sodium salt |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2013 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.6→64.99 Å / Num. obs: 44264 / % possible obs: 98.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 27.38 Å2 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.025 / Net I/σ(I): 15 / Num. measured all: 194222 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U0P Resolution: 1.6→64.988 Å / FOM work R set: 0.7454 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.88 / Stereochemistry target values: ML
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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 max: 104.88 Å2 / Biso mean: 36.78 Å2 / Biso min: 19.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→64.988 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
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