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Yorodumi- PDB-2y4g: Structure of the Tirandamycin-bound FAD-dependent tirandamycin ox... -
+Open data
-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 | ||||||
Components | TAMLTetra-amido macrocyclic ligand | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOMYCES SP. 307-9 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Carlson, J.C. / Li, S. / Gunatilleke, S.S. / Anzai, Y. / Burr, D.A. / Podust, L.M. / Sherman, D.H. | ||||||
Citation | Journal: Nat.Chem / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y4g.cif.gz | 447.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y4g.ent.gz | 362.7 KB | Display | PDB format |
PDBx/mmJSON format | 2y4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/2y4g ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y4g | HTTPS FTP |
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-Related structure data
Related structure data | 2y08SC 2y3rC 2y3sC C: citing same article (ref.) S: Starting model for refinement |
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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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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: |
-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.) STREPTOMYCES SP. 307-9 (bacteria) / Plasmid: PSJ2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RP / References: UniProt: D3Y1I2 |
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-Non-polymers , 6 types, 797 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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