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- PDB-3r3f: Crystal structure of Arthrobacter sp. strain SU 4-hydroxybenzoyl ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3r3f | ||||||
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Title | Crystal structure of Arthrobacter sp. strain SU 4-hydroxybenzoyl CoA thioesterase mutant T77A complexed with 4-hydroxyphenacyl CoA | ||||||
![]() | 4-hydroxybenzoyl-CoA thioesterase | ||||||
![]() | HYDROLASE / THIOESTERASE / HOTDOG-fold / 4-Hydroxybenzoyl-CoA | ||||||
Function / homology | ![]() 4-hydroxybenzoyl-CoA thioesterase / 4-hydroxybenzoyl-CoA thioesterase activity / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / phylloquinone biosynthetic process / menaquinone biosynthetic process / peroxisome / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Holden, H.M. / Thoden, J.B. / Song, F. / Zhuang, Z. / Trujillo, M. / Dunaway-Mariano, D. | ||||||
![]() | ![]() Title: The Catalytic Mechanism of the Hotdog-fold Enzyme Superfamily 4-Hydroxybenzoyl-CoA Thioesterase from Arthrobacter sp. Strain SU. Authors: Song, F. / Thoden, J.B. / Zhuang, Z. / Latham, J. / Trujillo, M. / Holden, H.M. / Dunaway-Mariano, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.9 KB | Display | ![]() |
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PDB format | ![]() | 56.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 915.8 KB | Display | ![]() |
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Full document | ![]() | 922.1 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3r32C ![]() 3r34C ![]() 3r35C ![]() 3r36C ![]() 3r37C ![]() 3r3aC ![]() 3r3bC ![]() 3r3cC ![]() 3r3dC ![]() 3teaC ![]() 1q4sS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 16386.402 Da / Num. of mol.: 2 / Mutation: T77A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q04416, 4-hydroxybenzoyl-CoA thioesterase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG3400, 200 mM LiCl, 100 mM MOPS, 1 mM 4-HYDROXYPHENACYL COA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Sep 23, 2002 / Details: goebel mirrors |
Radiation | Monochromator: ni-filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. all: 40350 / Num. obs: 40350 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2037 / Rsym value: 0.301 / % possible all: 66.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1q4s Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.596 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 24.615 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.796 Å / Total num. of bins used: 20
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