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- PDB-6gmg: Structure of a glutamine donor mimicking inhibitory peptide shape... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gmg | ||||||
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Title | Structure of a glutamine donor mimicking inhibitory peptide shaped by the catalytic cleft of microbial transglutaminase | ||||||
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![]() | TRANSFERASE / transglutaminase / Streptomyces mobaraensis / peptidic inhibitors / enzyme peptide interaction | ||||||
Function / homology | ![]() negative regulation of peptidase activity / protein-glutamine gamma-glutamyltransferase activity / cysteine-type endopeptidase inhibitor activity / serine-type endopeptidase inhibitor activity / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Schmelz, S. / Juettner, N.E. / Fuchsbauer, H.L. / Scrima, A. | ||||||
![]() | ![]() Title: Structure of a glutamine donor mimicking inhibitory peptide shaped by the catalytic cleft of microbial transglutaminase. Authors: Juettner, N.E. / Schmelz, S. / Kraemer, A. / Knapp, S. / Becker, B. / Kolmar, H. / Scrima, A. / Fuchsbauer, H.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.3 KB | Display | ![]() |
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PDB format | ![]() | 119.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.5 KB | Display | ![]() |
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Full document | ![]() | 482.1 KB | Display | |
Data in XML | ![]() | 28.4 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iu4S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37918.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: M3C567 #2: Protein/peptide | Mass: 1004.178 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: chloroacetylated serine peptide derived from SPI aa1-10, Glutamin6 was replace by a chloroacetylated serine Source: (synth.) ![]() #3: Chemical | ChemComp-FLC / | #4: Chemical | ChemComp-PEG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.67 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop Details: 38% v/v PEG400, 70 mM di-Sodium hydrogen phosphate, 100 mM Sodium phosphate citrate, pH 4.4 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 14, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→47 Å / Num. obs: 35089 / % possible obs: 98.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.71 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.08 / Rrim(I) all: 0.212 / Net I/σ(I): 8.1 / Num. measured all: 241385 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1iu4 Resolution: 2.25→47.001 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.05 Å2 / Biso mean: 25.9491 Å2 / Biso min: 11.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→47.001 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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