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- PDB-6ahi: Crystal structure of O-acetylserine dependent cystathionine beta-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ahi | |||||||||
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Title | Crystal structure of O-acetylserine dependent cystathionine beta-synthase from Helicobacter pylori. | |||||||||
![]() | Cysteine synthase | |||||||||
![]() | TRANSFERASE | |||||||||
Function / homology | ![]() cysteine synthase / cystathionine beta-synthase activity / cysteine biosynthetic process / cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tarique, F.K. / Devi, S. / Rehman, S.A.A. | |||||||||
![]() | ![]() Title: Identification and characterization of Helicobacter pylori O-acetylserine-dependent cystathionine beta-synthase, a distinct member of the PLP-II family. Authors: Devi, S. / Tarique, K.F. / Ali, M.F. / Abdul Rehman, S.A. / Gourinath, 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 | ![]() | 249.7 KB | Display | ![]() |
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PDB format | ![]() | 200 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.9 KB | Display | ![]() |
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Full document | ![]() | 462.6 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1z7wS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 306 / Label seq-ID: 1 - 306
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Components
#1: Protein | Mass: 34273.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700392 / 26695 / Gene: cysM, cysK, HP_0107 Production host: ![]() ![]() Strain (production host): BL21(DE3) / References: UniProt: P56067, cysteine synthase #2: Chemical | ChemComp-MET / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.46 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: Peg20K-Peg550MME 15%, 0.09M Amino acids mixture, 0.1M Mes-Imadazole buffer pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 45368 / % possible obs: 100 % / Redundancy: 16.3 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 47 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.862 / Num. unique obs: 2244 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Z7W Resolution: 1.9→48.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 8.444 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.455 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→48.12 Å
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Refine LS restraints |
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