[English] 日本語
Yorodumi- PDB-5jis: The Crystal Structure of O-acetyl serine sulfhydralase from Bruce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jis | ||||||
---|---|---|---|---|---|---|---|
Title | The Crystal Structure of O-acetyl serine sulfhydralase from Brucella abortus | ||||||
Components | Cysteine synthase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information cysteine biosynthetic process from serine / transferase activity, transferring alkyl or aryl (other than methyl) groups Similarity search - Function | ||||||
Biological species | Brucella abortus S19 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dharavath, S. / Gourinath, S. | ||||||
Citation | Journal: Biochem. J. / Year: 2017 Title: Structure-based mutational studies of O-acetylserine sulfhydrylase reveal the reason for the loss of cysteine synthase complex formation in Brucella abortus Authors: Dharavath, S. / Raj, I. / Gourinath, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jis.cif.gz | 266.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jis.ent.gz | 215.2 KB | Display | PDB format |
PDBx/mmJSON format | 5jis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/5jis ftp://data.pdbj.org/pub/pdb/validation_reports/ji/5jis | HTTPS FTP |
---|
-Related structure data
Related structure data | 5jjcC 1o58S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38038.742 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus S19 (bacteria) / Strain: S19 / Gene: BAbS19_I09950 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6AQU1, cysteine synthase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.48 % / Description: Diamond shaped |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 6.5 / Details: sodium cacodylate, potassium bromide, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 75389 / % possible obs: 99.9 % / Redundancy: 4.7 % / Net I/σ(I): 12.41 |
Reflection shell | Resolution: 2.2→2.24 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1o58 Resolution: 2.2→40.068 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.857 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.005 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→40.068 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|