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- PDB-4iyo: Crystal structure of cystathionine gamma lyase from Xanthomonas o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4iyo | |||||||||
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Title | Crystal structure of cystathionine gamma lyase from Xanthomonas oryzae pv. oryzae (XometC) in complex with E-site serine, A-site serine, A-site external aldimine structure with aminoacrylate and A-site iminopropionate intermediates | |||||||||
![]() | (Cystathionine gamma-lyase-like ...![]() | |||||||||
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Function / homology | ![]() carbon-sulfur lyase activity / ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ngo, H.P.T. / Kim, J.K. / Kang, L.W. | |||||||||
![]() | ![]() Title: PLP undergoes conformational changes during the course of an enzymatic reaction. Authors: Ngo, H.P. / Cerqueira, N.M. / Kim, J.K. / Hong, M.K. / Fernandes, P.A. / Ramos, M.J. / Kang, L.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 324.9 KB | Display | ![]() |
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PDB format | ![]() | 260.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ixsC ![]() 4ixzSC ![]() 4iy7C C: citing same article ( 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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Details | BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC SOFTWARE USED: PISA TOTAL BURIED SURFACE AREA: 21500 ANGSTROM**2 SURFACE AREA OF THE COMPLEX: 41940 ANGSTROM**2 CHANGE IN SOLVENT FREE ENERGY: -128.0 KCAL/MOL APPLY THE FOLLOWING TO CHAINS: A, B, C, D BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 |
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Components
-Cystathionine gamma-lyase-like ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 42635.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: KACC 10331/KXO85 / Gene: metB, XOCGL, XOO0778 / Production host: ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 42863.695 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: KACC 10331/KXO85 / Gene: metB, XOCGL, XOO0778 / Production host: ![]() ![]() ![]() ![]() |
-Non-polymers , 7 types, 1337 molecules ![](data/chem/img/SER.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/0JO.gif)
![](data/chem/img/NAK.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/0JO.gif)
![](data/chem/img/NAK.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SER / ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-SO4 / | ![]() #6: Chemical | ChemComp-0JO / | #7: Chemical | #8: Chemical | ChemComp-PYR / | ![]() #9: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.44 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 25.5% PEG4000, 0.17M LITHIUM SULFATE, 0.085M TRIS, 15% GLYCEROL, PH 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.78→50 Å / Num. obs: 142510 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.78→1.81 Å / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4IXZ Resolution: 1.8→33.82 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.021 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→33.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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