[English] 日本語
Yorodumi- PDB-4zu6: Crystal Structure of O-Acetylserine Sulfhydrylase from Haemophilu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zu6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
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 | |||||||||
Components |
| |||||||||
Keywords | Transferase/Transferase Inhibitor / Amino Acid biosynthesis / cysteine biosynthesis / pyridoxial phosphate / Transferase / Transferase-Transferase Inhibitor complex | |||||||||
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 KW20 (bacteria) Salmonella typhimurium LT2 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | |||||||||
Authors | Ekka, M.K. / Singh, A.K. / Kaushik, A. / Kumaran, S. | |||||||||
Citation | Journal: To Be Published Title: Crystal Structure of O-Acetylserine Sulfhydrylase from Haemophilus inuen-zae in complex with pre-reactive o-acetyl serine and peptide inhibitor Authors: Ekka, M.K. / Singh, A.K. / Kaushik, A. / Kumaran, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4zu6.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4zu6.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 4zu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/4zu6 ftp://data.pdbj.org/pub/pdb/validation_reports/zu/4zu6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ho1S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35232.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae KW20 (bacteria) / Strain: KW20 / Gene: cysK, HI_1103 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45040, cysteine synthase |
---|---|
#2: Protein/peptide | Mass: 1177.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Salmonella typhimurium LT2 (bacteria) / References: UniProt: P29847 |
#3: Chemical | ChemComp-OAS / |
#4: Chemical | ChemComp-PLP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.25 % / Description: Triangle shaped |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES, 1.4M sodium citrate / PH range: 7.4-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: continous |
---|---|
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: Jul 13, 2011 |
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: 2.03→35.5 Å / Num. obs: 17815 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Biso Wilson estimate: 31.04 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 51 |
Reflection shell | Resolution: 2.03→2.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 8.64 / % possible all: 92 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HO1 Resolution: 2.03→20 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.43 / 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: 2.03→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|