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Yorodumi- PDB-4amn: Crystal Structure of the Acyltransferase Domain of the Iterative ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4amn | ||||||
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Title | Crystal Structure of the Acyltransferase Domain of the Iterative Polyketide Synthase in Enediyne Biosynthesis Reveals the Molecular Basis of Substrate Specificity | ||||||
Components | DYNE8 | ||||||
Keywords | TRANSFERASE / POLYKETIDE SYNTHASE / ACYLTRANSFERASE / DYNEMICIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | MICROMONOSPORA CHERSINA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Liew, C.W. / Lescar, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Crystal Structure of the Acyltransferase Domain of the Iterative Polyketide Synthase in Enediyne Biosynthesis. Authors: Liew, C.W. / Nilsson, M. / Chen, M.W. / Sun, H. / Cornvik, T. / Liang, Z. / Lescar, J. #1: Journal: Nat.Prod.Rep. / Year: 2010 Title: Complexity and Simplicity in the Biosynthesis of Enediyne Natural Products. Authors: Liang, Z.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4amn.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4amn.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 4amn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4amn ftp://data.pdbj.org/pub/pdb/validation_reports/am/4amn | HTTPS FTP |
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-Related structure data
Related structure data | 4ammSC 4amoC 4ampC 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
#1: Protein | Mass: 42944.539 Da / Num. of mol.: 1 / Fragment: AT DOMAIN, RESIDUES 473-893 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MICROMONOSPORA CHERSINA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA T1R / References: UniProt: Q84HI8 | ||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.99 % |
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Crystal grow | pH: 8.5 / Details: 0.1 M TRIS-CL PH 8.0, 30% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 13, 2011 / Details: COLLIMATOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→18.8 Å / Num. obs: 54690 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.5→1.5 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.5 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AMM Resolution: 1.5→52.42 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU B: 1.25 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 18.129 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→52.42 Å
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Refine LS restraints |
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