[English] 日本語
Yorodumi- PDB-4li3: Crystal Structure of O-Acetylserine Sulfhydrylase from Haemophilu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4li3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of O-Acetylserine Sulfhydrylase from Haemophilus influenzae in complex with high affinity inhibitory peptide from Serine acetyl transferase of Salmonella typhimurium | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / alpha/beta fold / Rossmann fold / catalytic activity / cysteine synthase activity / serine acetyl transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex / Structural Genomics | ||||||
Function / homology | Function and homology information 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.592 Å | ||||||
Authors | Singh, A.K. / Ekka, M.K. / Kaushik, A. / Kumaran, S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of O-Acetylserine Sulfhydrylase from Haemophilus influenzae in complex with high affinity inhibitory peptide from Serine acetyl transferase of Salmonella typhimurium Authors: Singh, A.K. / Ekka, M.K. / Kaushik, A. / Kumaran, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4li3.cif.gz | 73.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4li3.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 4li3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/4li3 ftp://data.pdbj.org/pub/pdb/validation_reports/li/4li3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1y7lS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33651.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: IPTG inducible / Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC 51907 / Gene: cysK, HI_1103 / Plasmid: pET 28A / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P45040, cysteine synthase |
---|---|
#2: Protein/peptide | Mass: 900.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) Salmonella typhimurium (bacteria) / References: UniProt: F5ZW64, UniProt: P29847*PLUS |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.43 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 1.4M sodium Citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 2012 |
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: 2.59→43.1 Å / Num. all: 8700 / Num. obs: 8700 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 42.12 Å2 / Net I/σ(I): 19 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y7L Resolution: 2.592→43.01 Å / SU ML: 0.31 / Isotropic thermal model: Isotropic Model / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.13 / Stereochemistry target values: ML
| |||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.592→43.01 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
|