+Open data
-Basic information
Entry | Database: PDB / ID: 5m6q | ||||||
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Title | Crystal Structure of Kutzneria albida transglutaminase | ||||||
Components | Uncharacterized protein | ||||||
Keywords | TRANSFERASE / MTGASE / ZYMOGEN / PRO-ENZYME / CROSS-LINKING / ACYLTRANSFERASE | ||||||
Function / homology | Protein-glutamine gamma-glutamyltransferase / Protein-glutamine gamma-glutamyltransferase superfamily / Microbial transglutaminase / protein-glutamine gamma-glutamyltransferase activity / Papain-like cysteine peptidase superfamily / Uncharacterized protein Function and homology information | ||||||
Biological species | Kutzneria albida DSM 43870 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Steffen, W. / Benz, J. / Rudolph, M.G. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Discovery of a microbial transglutaminase enabling highly site-specific labeling of proteins. Authors: Steffen, W. / Ko, F.C. / Patel, J. / Lyamichev, V. / Albert, T.J. / Benz, J. / Rudolph, M.G. / Bergmann, F. / Streidl, T. / Kratzsch, P. / Boenitz-Dulat, M. / Oelschlaegel, T. / Schraeml, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m6q.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m6q.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 5m6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m6q_validation.pdf.gz | 458.3 KB | Display | wwPDB validaton report |
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Full document | 5m6q_full_validation.pdf.gz | 463.2 KB | Display | |
Data in XML | 5m6q_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 5m6q_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/5m6q ftp://data.pdbj.org/pub/pdb/validation_reports/m6/5m6q | HTTPS FTP |
-Related structure data
Related structure data | 3iu0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26489.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kutzneria albida DSM 43870 (bacteria) / Gene: KALB_7456 / Plasmid: based on pQE-80 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Tuner / References: UniProt: W5WHY8 #2: Chemical | ChemComp-MES / #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.76 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium tartrate, 20% PEG 3350 / PH range: unknown |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.98→47.96 Å / Num. obs: 49849 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.91 % / Biso Wilson estimate: 35.381 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.179 / Net I/σ(I): 7.41 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3iu0 Resolution: 1.98→46.276 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 94.4 Å2 / Biso mean: 33.3266 Å2 / Biso min: 15.57 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.98→46.276 Å
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