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Yorodumi- PDB-1nug: Role of Calcium Ions in the Activation and Activity of the Transg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nug | ||||||
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Title | Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 calciums, 1 Mg, inactive form) | ||||||
Components | Protein-glutamine glutamyltransferase E | ||||||
Keywords | TRANSFERASE / Transglutaminase 3 / metalloenzyme / calcium ion | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Ahvazi, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Roles of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme Authors: Ahvazi, B. / Boeshans, K.M. / Idler, W. / Baxa, U. / Steinert, P.M. #1: Journal: Embo J. / Year: 2002 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. #2: Journal: J.Struct.Biol. / Year: 2001 Title: Crystallization and Preliminary X-ray Analysis of Human Transglutaminase 3 from Zymogen to Active Form Authors: Kim, H.C. / Nemes, Z. / Idler, W.W. / Hyde, C.C. / Steinert, P.M. / Ahvazi, B. | ||||||
History |
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Remark 400 | COMPOUND THE ENZYME WAS PROTEOLYZED WITH DISPASE I FOR ACTIVATION, MONOQ PURIFIED AND ACTIVATED ...COMPOUND THE ENZYME WAS PROTEOLYZED WITH DISPASE I FOR ACTIVATION, MONOQ PURIFIED AND ACTIVATED WITH CACL2. THE MGCL2 AND ATP SALT WAS USED TO INHIBIT THE ACTIVITY. | ||||||
Remark 999 | SEQUENCE The following residues are noted as conflicts in the Swiss-Prot database: K562R, G654R ...SEQUENCE The following residues are noted as conflicts in the Swiss-Prot database: K562R, G654R (sequence database numbering). According to the author, residue 251 (sequence database numbering) is Asp and does not represent a mutation but a mistake in the Swiss-Prot database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nug.cif.gz | 286.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nug.ent.gz | 228.3 KB | Display | PDB format |
PDBx/mmJSON format | 1nug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nug_validation.pdf.gz | 382.9 KB | Display | wwPDB validaton report |
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Full document | 1nug_full_validation.pdf.gz | 411 KB | Display | |
Data in XML | 1nug_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 1nug_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/1nug ftp://data.pdbj.org/pub/pdb/validation_reports/nu/1nug | HTTPS FTP |
-Related structure data
Related structure data | 1nudC 1nufC 1l9nS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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 Source: (gene. exp.) Homo sapiens (human) / Gene: TGM3 / Plasmid: Bac-N_Blue, Invitrogen / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q08188, protein-glutamine gamma-glutamyltransferase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-CA / #4: Chemical | #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: 2.86 Å3/Da / Density % sol: 57.05 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM NaCl, 100 mM NaHEPES (pH 7.5) 4-8% Peg 4K, VAPOR DIFFUSION, HANGING DROP, temperature 288K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→20 Å / Num. obs: 65766 / % possible obs: 10.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.1 Å2 | ||||||||||||||||||
Reflection shell | Resolution: 2.4→2.55 Å / % possible all: 97.7 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 25 Å / % possible obs: 98.3 % / Num. measured all: 495285 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 97.7 % / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1L9N Resolution: 2.4→20 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.011
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Refinement | *PLUS Lowest resolution: 25 Å / % reflection Rfree: 10 % | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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