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- PDB-5kp8: Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kp8 | |||||||||
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Title | Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthase in Complex with Acetyl Donor-ACP | |||||||||
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![]() | TRANSFERASE / HMG synthase / enzyme-ACP complex | |||||||||
Function / homology | ![]() hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / acetyl-CoA metabolic process / ergosterol biosynthetic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Maloney, F.P. / Smith, J.L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Anatomy of the beta-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate. Authors: Maloney, F.P. / Gerwick, L. / Gerwick, W.H. / Sherman, D.H. / Smith, J.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 209.2 KB | Display | ![]() |
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PDB format | ![]() | 166.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 974.4 KB | Display | ![]() |
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Full document | ![]() | 977 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 30.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kp5SC ![]() 5kp6SC ![]() 5kp7C S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 49225.617 Da / Num. of mol.: 1 / Fragment: unp residues 17-76 / Mutation: C114S, K368A, Q369A, Q371A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: F4Y432, hydroxymethylglutaryl-CoA synthase |
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#2: Protein | Mass: 11452.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-PNS / |
#4: Chemical | ChemComp-6VG / ~{ |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 6% PEG 8000, 100 mM (NH4)2SO4, 1X MMT pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2014 |
Radiation | Monochromator: crystal monochromator and K-B pair of biomorph mirrors Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→87.38 Å / Num. obs: 48869 / % possible obs: 100 % / Redundancy: 19.5 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 16.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KP5, 5KP6 Resolution: 1.9→87.38 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 5.387 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→87.38 Å
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Refine LS restraints |
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