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- PDB-2y4g: Structure of the Tirandamycin-bound FAD-dependent tirandamycin ox... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y4g | ||||||
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Title | Structure of the Tirandamycin-bound FAD-dependent tirandamycin oxidase TamL in P212121 space group | ||||||
![]() | TAML | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Carlson, J.C. / Li, S. / Gunatilleke, S.S. / Anzai, Y. / Burr, D.A. / Podust, L.M. / Sherman, D.H. | ||||||
![]() | ![]() Title: Tirandamycin Biosynthesis is Mediated by Co-Dependent Oxidative Enzymes Authors: Carlson, J.C. / Li, S. / Gunatilleke, S.S. / Anzai, Y. / Burr, D.A. / Podust, L.M. / Sherman, D.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 447.3 KB | Display | ![]() |
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PDB format | ![]() | 362.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 48.2 KB | Display | |
Data in CIF | ![]() | 70.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y08SC ![]() 2y3rC ![]() 2y3sC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 5 - 495 / Label seq-ID: 35 - 525
NCS oper: (Code: given Matrix: (-0.7723, 0.01993, -0.6349), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 58189.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COVALENT LINK BETWEEN 8-ALPHA METHYL GROUP OF FAD TO N-1 OF HIS 62. COVALENT LINK BETWEEN C-6 ATOM OF FAD AND CYS 122. Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 797 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/TIR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/TIR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | FLAVIN ADENINE DINUCLEOTIDE (FAD): COVALENT LINK BETWEEN 8-ALPHA METHYL GROUP OF FAD TO N-1 OF H62. ...FLAVIN ADENINE DINUCLEOTI |
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Sequence details | HIS8-TAG AND TEV PROTEASE SITE ARE ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.84 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 15% PEG 4000, 0.1M MGCL2, 0.1M HEPES 7.5, ADDITIVE 0.1M MGCL2. |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→134.54 Å / Num. obs: 67342 / % possible obs: 91.7 % / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.03→2.14 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.5 / % possible all: 63 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y08 Resolution: 2.03→134.54 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.914 / SU B: 10.334 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE SIDECHAIN ATOMS WITH MISSING ELECTRON DENSITY WERE NOT BUILT.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.732 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→134.54 Å
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Refine LS restraints |
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