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- PDB-2w3x: Crystal structure of a bifunctional hotdog fold thioesterase in e... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2w3x | ||||||
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Title | Crystal structure of a bifunctional hotdog fold thioesterase in enediyne biosynthesis, CalE7 | ||||||
![]() | CALE7 | ||||||
![]() | HYDROLASE / HOTDOG FOLD / THIOESTERASE / ENEDIYNE BIOSYNTHESIS | ||||||
Function / homology | ![]() Thioesterase-like superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kotaka, M. / Kong, R. / Qureshi, I. / Ho, Q.S. / Sun, H. / Liew, C.W. / Goh, L.P. / Cheung, P. / Mu, Y. / Lescar, J. / Liang, Z.X. | ||||||
![]() | ![]() Title: Structure and Catalytic Mechanism of the Thioesterase Cale7 in Enediyne Biosynthesis. Authors: Kotaka, M. / Kong, R. / Qureshi, I. / Ho, Q.S. / Sun, H. / Liew, C.W. / Goh, L.P. / Cheung, P. / Mu, Y. / Lescar, J. / Liang, Z.X. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.2 KB | Display | ![]() |
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PDB format | ![]() | 156.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 823.6 KB | Display | ![]() |
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Full document | ![]() | 842.2 KB | Display | |
Data in XML | ![]() | 40.2 KB | Display | |
Data in CIF | ![]() | 56.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2egiS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 17154.803 Da / Num. of mol.: 6 / Fragment: RESIDUES 1-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 533 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/JEF.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/JEF.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-JEF / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | JEFFAMINE (JEF): ONLY A FRAGMENT OF JEFFAMINE IS SEEN IN THE STRUCTURE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.2 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.1 NA HEPES PH7.0, 28% JEFFAMINE-M600 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072121 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 90879 / % possible obs: 99.3 % / Observed criterion σ(I): -1 / Redundancy: 3.6 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.2 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2EGI Resolution: 1.75→29.68 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2342525.2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.57 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→29.68 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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