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Yorodumi- PDB-1q4u: Crystal structure of 4-hydroxybenzoyl CoA thioesterase from arthr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q4u | ||||||
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Title | Crystal structure of 4-hydroxybenzoyl CoA thioesterase from arthrobacter sp. strain SU complexed with 4-hydroxybenzyl CoA | ||||||
Components | Thioesterase | ||||||
Keywords | HYDROLASE / thioesterase / hot-dog | ||||||
Function / homology | Function and homology information 4-hydroxybenzoyl-CoA thioesterase / 4-hydroxybenzoyl-CoA thioesterase activity / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / cytosol Similarity search - Function | ||||||
Biological species | Arthrobacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Thoden, J.B. / Zhuang, Z. / Dunaway-Mariano, D. / Holden, H.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The Structure of 4-Hydroxybenzoyl-CoA Thioesterase from Arthrobacter sp. strain SU Authors: Thoden, J.B. / Zhuang, Z. / Dunaway-Mariano, D. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q4u.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q4u.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 1q4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q4u_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1q4u_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1q4u_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 1q4u_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/1q4u ftp://data.pdbj.org/pub/pdb/validation_reports/q4/1q4u | HTTPS FTP |
-Related structure data
Related structure data | 1q4sC 1q4tSC C: citing same article (ref.) S: Starting model for refinement |
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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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Details | homotetramer; The tetramer is generated from the crystallographically independent dimer by rotation about the crystallographic 2-fold axis |
-Components
#1: Protein | Mass: 16416.428 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter sp. (bacteria) / Strain: SU / Gene: FCBC / Plasmid: pET23b / Production host: Escherichia coli (E. coli) References: UniProt: Q04416, 4-hydroxybenzoyl-CoA thioesterase #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.77 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG-3400, MOPS, LiCl, KCl, 4-hydroxybenzyl CoA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: May 30, 2002 / Details: goebel optics |
Radiation | Monochromator: goebel optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 57216 / Num. obs: 57216 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.041 / Net I/σ(I): 39.1 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 5007 / Rsym value: 0.296 / % possible all: 86.3 |
Reflection | *PLUS Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS % possible obs: 86.3 % / Num. unique obs: 5007 / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1Q4T Resolution: 1.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 51034 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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