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Open data
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Basic information
Entry | Database: PDB / ID: 5nry | |||||||||
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Title | Cys-Gly dipeptidase GliJ in complex with Fe3+ | |||||||||
![]() | Dipeptidase gliJ | |||||||||
![]() | HYDROLASE / carboxypeptidase / dipeptidase / gliotoxin biosynthesis | |||||||||
Function / homology | ![]() symbiont-mediated suppression of host immune response / gliotoxin biosynthetic process / membrane dipeptidase / mycotoxin biosynthetic process / metallodipeptidase activity / proteolysis / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Groll, M. / Huber, E.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Gliotoxin Biosynthesis: Structure, Mechanism, and Metal Promiscuity of Carboxypeptidase GliJ. Authors: Marion, A. / Groll, M. / Scharf, D.H. / Scherlach, K. / Glaser, M. / Sievers, H. / Schuster, M. / Hertweck, C. / Brakhage, A.A. / Antes, I. / Huber, E.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.2 KB | Display | ![]() |
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PDB format | ![]() | 142.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.6 KB | Display | ![]() |
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Full document | ![]() | 419.7 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lwzC ![]() 5lx0SC ![]() 5lx1C ![]() 5lx4C ![]() 5lx7C ![]() 5nrtC ![]() 5nruC ![]() 5nrxC ![]() 5nrzC ![]() 5ns1C ![]() 5ns2C ![]() 5ns5C 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45008.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0, 5% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.73842 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→45 Å / Num. obs: 98319 / % possible obs: 98.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.6 / % possible all: 93.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LX0 Resolution: 1.85→15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.91 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.095 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.255 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→15 Å
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Refine LS restraints |
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