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- PDB-1lo9: X-ray crystal structure of 4-hydroxybenzoyl CoA thioesterase muta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lo9 | ||||||
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Title | X-ray crystal structure of 4-hydroxybenzoyl CoA thioesterase mutant D17N complexed with 4-hydroxybenzoyl CoA | ||||||
![]() | 4-hydroxybenzoyl-CoA Thioesterase | ||||||
![]() | HYDROLASE / Thioesterase / hot dog fold / catalytic mechanism | ||||||
Function / homology | ![]() 4-hydroxybenzoyl-CoA thioesterase / 4-hydroxybenzoyl-CoA thioesterase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thoden, J.B. / Holden, H.M. / Zhuang, Z. / Dunaway-Mariano, D. | ||||||
![]() | ![]() Title: X-ray crystallographic analyses of inhibitor and substrate complexes of wild-type and mutant 4-hydroxybenzoyl-CoA thioesterase. Authors: Thoden, J.B. / Holden, H.M. / Zhuang, Z. / 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 | ![]() | 43.9 KB | Display | ![]() |
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PDB format | ![]() | 29.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 730.7 KB | Display | ![]() |
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Full document | ![]() | 740.9 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lo7C ![]() 1lo8C ![]() 1bvqS 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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Details | The biological assembly is a homotetramer. The single independent monomer in the asymmetric unit sits on 222 site symmetry. Matrices to generate the tetramer are as follows: (1) -1 0 0 0 -1 0 0 0 1 52.5 0.0 0.0 (2) -1 0 0 0 1 0 0 0 -1 52.5 0.0 0.0 (3) 1 0 0 0 -1 0 0 0 -1 0.0 0.0 0.0 |
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Components
#1: Protein | Mass: 16139.466 Da / Num. of mol.: 1 / Mutation: D17N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P56653, 4-hydroxybenzoyl-CoA thioesterase |
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#2: Chemical | ChemComp-BCA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.12 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: batch / pH: 6 Details: PEG 5000-O-methylether, potassium chloride, MES, 4-hydroxybenzoyl CoA, pH 6.0, batch at 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: sparse matrix screening | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 275 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 16, 2001 / Details: goebel mirrors |
Radiation | Monochromator: goebel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 3068 / Num. obs: 3068 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rsym value: 0.078 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.8→2.93 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 349 / Rsym value: 0.285 / % possible all: 77.6 |
Reflection | *PLUS Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 77.6 % / Num. unique obs: 349 / Rmerge(I) obs: 0.285 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BVQ Resolution: 2.8→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 2761 / Rfactor all: 0.148 / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.148 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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