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- PDB-1l9n: Three-dimensional structure of the human transglutaminase 3 enzym... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1l9n | ||||||
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Title | Three-dimensional structure of the human transglutaminase 3 enzyme: binding of calcium ions change structure for activation | ||||||
![]() | Protein-glutamine glutamyltransferase E3 | ||||||
![]() | TRANSFERASE / Activation / Calcium binding / transglutaminase | ||||||
Function / homology | ![]() protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / hair follicle morphogenesis / acyltransferase activity / keratinization / extrinsic component of cytoplasmic side of plasma membrane / catalytic activity / keratinocyte differentiation / protein modification process ...protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / hair follicle morphogenesis / acyltransferase activity / keratinization / extrinsic component of cytoplasmic side of plasma membrane / catalytic activity / keratinocyte differentiation / protein modification process / calcium ion binding / structural molecule activity / protein-containing complex / extracellular exosome / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ahvazi, B. | ||||||
![]() | ![]() Title: Three-dimensional structure of the human transglutaminase 3 enzyme: binding of calcium ions changes structure for activation. Authors: Ahvazi, B. / Kim, H.C. / Kee, S.H. / Nemes, Z. / Steinert, P.M. #1: ![]() Title: Two non-proline cis peptide bonds may be important for factor XIII function Authors: Yee, V.C. / Pedersen, L.C. / Le Trong, I. / Bishop, P.D. / Stenkamp, R.E. / Teller, D.C. #2: ![]() Title: Three-dimensional structure of a transglutaminase: human blood coagulation factor XII Authors: Weiss, M.S. / Metzner, H.J. / Hilgenfeld, R. | ||||||
History |
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Remark 999 | The following residues are noted as conflicts in the Swiss-Prot database: T13K, K562R, G654R. ... The following residues are noted as conflicts in the Swiss-Prot database: T13K, K562R, G654R. According to the author, residue 250 is Asp and does not represent a mutation but a mistake in the Swiss-Prot database. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 295.4 KB | Display | ![]() |
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PDB format | ![]() | 233.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1l9mSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 76670.500 Da / Num. of mol.: 2 / Mutation: F264L Source method: isolated from a genetically manipulated source Details: This sequence occurs naturally in humans / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q08188, protein-glutamine gamma-glutamyltransferase #2: Sugar | #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.51 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 4-12% (w/v) Peg 6K, 100 mM Bicine (pH 9) and 1% dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 26, 2000 / Details: mirrors |
Radiation | Monochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 80238 / Num. obs: 80238 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.8 Å2 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.1→20 Å / % possible all: 91.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 558858 |
Reflection shell | *PLUS Lowest resolution: 2.17 Å / % possible obs: 91.8 % / Mean I/σ(I) obs: 4.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB-ID 1L9M zymogen transglutaminase Resolution: 2.1→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: NCS two fold averaging was employed during refinement but at the later stage the NCS was released
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Displacement parameters | Biso mean: 26 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor all: 0.276 / Rfactor obs: 0.1887 / Rfactor Rfree: 0.2334 / Rfactor Rwork: 0.1887 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.276 / Rfactor Rwork: 0.241 / Rfactor obs: 0.241 |