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- PDB-5dbe: Crystal structure of O-acetylserine sulfhydrylase from Haemophilu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dbe | |||||||||
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Title | Crystal structure of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with pre-reactive O-acetyl serine, alpha-aminoacrylate reaction intermediate and peptide inhibitor at the resolution of 2.25A | |||||||||
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![]() | TRANSFERASE/TRANSFERASE INHIBITOR / AMINO-ACID BIOSYNTHESIS / CYSTEINE BIOSYNTHESIS / TRANSFERASE / PYRIDOXAL PHOSPHATE / TRANSFERASE-TRANSFERASE INHIBITOR COMP / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | ![]() serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine synthase / cystathionine beta-synthase activity / cysteine synthase activity / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Singh, A.K. / Kaushik, A. / Ekka, M.K. / Kumaran, S. | |||||||||
![]() | ![]() Title: Crystal Structure Of O-Acetylserine Sulfhydrylase From Haemophilus Influenzae In Complex With Pre-Reactive O-Acetyl Serine, Alpha-Aminoacrylate Reactionintermediate And Peptide Inhibitor At The Resolution Of 2.25A Authors: Singh, A.K. / Kaushik, A. / Ekka, M.K. / Kumaran, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76 KB | Display | ![]() |
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PDB format | ![]() | 52.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 850.7 KB | Display | ![]() |
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Full document | ![]() | 857.1 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ho1S 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
-Protein / Protein/peptide , 2 types, 2 molecules XA
#1: Protein | Mass: 35232.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Details (production host): kanamycin resisitant gene, iptg inducble, N erminal His tag Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 1177.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 48 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/OAS.gif)
![](data/chem/img/0JO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OAS.gif)
![](data/chem/img/0JO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-OAS / | #5: Chemical | ChemComp-0JO / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 40 % / Description: TRIANGLE SHAPED |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion Details: 0.1M HEPES, 1.2M SODIUM CITRATE, VAPOR DIFFUSION, SITTING DROP PH range: 7.4-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2011 / Details: vaimax Hf optics |
Radiation | Monochromator: GRAPHITE POLAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→35 Å / Num. obs: 13894 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 42.8 |
Reflection shell | Resolution: 2.25→2.35 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 8.6 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4HO1 Resolution: 2.25→35 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→35 Å
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Refine LS restraints |
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LS refinement shell |
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