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Yorodumi- PDB-4amo: Crystal Structure of the Acyltransferase Domain of the Iterative ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4amo | ||||||
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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 / ENEDIYNE / DYNEMICIN | ||||||
Function / homology | Function and homology information DIM/DIP cell wall layer assembly / fatty acid synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | MICROMONOSPORA CHERSINA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 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 | 4amo.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4amo.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 4amo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4amo_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 4amo_full_validation.pdf.gz | 454.2 KB | Display | |
Data in XML | 4amo_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 4amo_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4amo ftp://data.pdbj.org/pub/pdb/validation_reports/am/4amo | HTTPS FTP |
-Related structure data
Related structure data | 4ammSC 4amnC 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: 42972.590 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 | #3: Water | ChemComp-HOH / | Sequence details | CODON OPTIMIZED FOR E.COLI EXPRESSION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.57 % |
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Crystal grow | pH: 8 / 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: X06SA / Wavelength: 1.072 |
Detector | Type: DECTRIS 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: 1.9→29.7 Å / Num. obs: 30505 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.9→1.9 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.1 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 4AMM Resolution: 1.9→29.66 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.94 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM 586 TO 615 ARE ABSENT FROM THE MODEL OWING 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: 28.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.66 Å
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Refine LS restraints |
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