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Yorodumi- PDB-4amp: Crystal Structure of the Acyltransferase Domain of the Iterative ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4amp | ||||||
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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 / DYNEMICIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | MICROMONOSPORA CHERSINA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 | 4amp.cif.gz | 90.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4amp.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 4amp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4amp ftp://data.pdbj.org/pub/pdb/validation_reports/am/4amp | HTTPS FTP |
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-Related structure data
Related structure data | 4ammSC 4amnC 4amoC 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) / Plasmid: PNIC28-BSA4-DYNE8-MICCE-EC019 / 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 | ChemComp-CL / |
#3: Chemical | ChemComp-MLI / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.2 % |
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Crystal grow | pH: 8 / Details: 0.1M TRIS-CL PH8.0, 30% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.072 |
Detector | Type: DECTRIS PIXEL PILATUS 2M-F / Detector: PIXEL / Date: Apr 13, 2011 / Details: COLLIMATOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→26.33 Å / Num. obs: 45596 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.65→1.65 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.8 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AMM Resolution: 1.65→52.5 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.783 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM 587 TO 615 ARE ABSENT FROM THE MODEL DUE TO POOR ELECTRON DENSITY.
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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: 24.924 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→52.5 Å
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Refine LS restraints |
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