+Open data
-Basic information
Entry | Database: PDB / ID: 5nrz | |||||||||
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Title | Cys-Gly dipeptidase GliJ in complex with Mn2+ | |||||||||
Components | Dipeptidase gliJ | |||||||||
Keywords | HYDROLASE / carboxypeptidase / dipeptidase / gliotoxin biosynthesis | |||||||||
Function / homology | Function and homology information 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 | Aspergillus fumigatus Af293 (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Groll, M. / Huber, E.M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: ACS Chem. Biol. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nrz.cif.gz | 177 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nrz.ent.gz | 139.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nrz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/5nrz ftp://data.pdbj.org/pub/pdb/validation_reports/nr/5nrz | HTTPS FTP |
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-Related structure data
Related structure data | 5lwzC 5lx0SC 5lx1C 5lx4C 5lx7C 5nrtC 5nruC 5nrxC 5nryC 5ns1C 5ns2C 5ns5C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Aspergillus fumigatus Af293 (mold) / Gene: gliJ, AFUA_6G09650 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4WMJ8, membrane dipeptidase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.53 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.89031 Å |
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: 1.89031 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→45 Å / Num. obs: 71550 / % possible obs: 99.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.05→2.15 Å / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.6 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LX0 Resolution: 2.05→15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 7.31 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.123 / 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: 44.14 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→15 Å
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Refine LS restraints |
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