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Yorodumi- PDB-7c9j: Transglutaminase from Geobacillus stearothermophilus (without C-t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c9j | ||||||
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Title | Transglutaminase from Geobacillus stearothermophilus (without C-terminal extension) | ||||||
Components | Protein-glutamine gamma-glutamyltransferase | ||||||
Keywords | TRANSFERASE / Transglutaminase | ||||||
Function / homology | Protein-glutamine gamma-glutamyltransferase, bacteria / protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / sporulation resulting in formation of a cellular spore / CITRIC ACID / Protein-glutamine gamma-glutamyltransferase Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Takita, T. / Mikami, B. / Lei, Y. / Jing, Y. / Yamada, A. / Yasukawa, K. | ||||||
Citation | Journal: To be published Title: Transglutaminase from Geobacillus stearothermophilus (without C-terminal extension) Authors: Takita, T. / Mikami, B. / Lei, Y. / Jing, Y. / Yamada, A. / Yamada, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c9j.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c9j.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 7c9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c9j_validation.pdf.gz | 461.7 KB | Display | wwPDB validaton report |
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Full document | 7c9j_full_validation.pdf.gz | 462.9 KB | Display | |
Data in XML | 7c9j_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 7c9j_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/7c9j ftp://data.pdbj.org/pub/pdb/validation_reports/c9/7c9j | HTTPS FTP |
-Related structure data
Related structure data | 4p8iS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29130.971 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: D9548_14210 / Production host: Escherichia coli (E. coli) References: UniProt: A0A3L7D5Y5, protein-glutamine gamma-glutamyltransferase | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CIT / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 20000, 2-(N-morpholino)ethanesulfonic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Dec 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 15940 / % possible obs: 98.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 44.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.047 / Net I/σ(I): 21.16 |
Reflection shell | Resolution: 2.1→2.22 Å / Redundancy: 2.98 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 4544 / CC1/2: 0.743 / Rrim(I) all: 0.618 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P8I Resolution: 2.1→39.45 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.18 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→39.45 Å
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Refine LS restraints |
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LS refinement shell |
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