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- PDB-3msg: Enzyme-Substrate interactions of IXT6, the intracellular xylanase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3msg | |||||||||
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Title | Enzyme-Substrate interactions of IXT6, the intracellular xylanase of G. stearothermophilus. | |||||||||
![]() | Intra-cellular xylanase ixt6 | |||||||||
![]() | HYDROLASE / xylanase | |||||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Solomon, V. / Zolotnitsky, G. / Alhadeff, R. / Shoham, Y. / Shoham, G. | |||||||||
![]() | ![]() Title: Enzyme-Substrate interactions of IXT6, the intracellular xylanase of G. stearothermophilus. Authors: Solomon, V. / Zolotnitsky, G. / Alhadeff, R. / Shoham, Y. / Shoham, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.1 KB | Display | ![]() |
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PDB format | ![]() | 129.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 32.4 KB | Display | |
Data in CIF | ![]() | 47.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ms8C ![]() 3msdC ![]() 3muaC ![]() 3muiC ![]() 2q8xS S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38694.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: T-6 / Gene: xynA2 / Plasmid: pET9d / Production host: ![]() ![]() |
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-Sugars , 2 types, 3 molecules ![](data/chem/img/XYP.gif)
#2: Polysaccharide | #3: Sugar | ChemComp-XYP / | |
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-Non-polymers , 4 types, 626 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M sodium cacodylate pH=6.5, 1.9M soduim acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→36.44 Å / Num. all: 162613 / Num. obs: 131154 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 11.4 / Redundancy: 6.76 % / Biso Wilson estimate: 21.2 Å2 / Rsym value: 0.069 / Net I/σ(I): 25.18 |
Reflection shell | Resolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2.07 / Num. unique all: 19553 / Rsym value: 0.495 / % possible all: 93.8 |
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Processing
Software |
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Refinement | Method to determine structure: The same IXT6 only with xylotiose, using rigid, annealing Starting model: 2Q8X Resolution: 1.5→36.44 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→36.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.53 Å / Rfactor Rfree error: 0.008
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