[English] 日本語
Yorodumi- PDB-8oxy: Transglutaminase 3 without calcium in complex with DH patient-der... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oxy | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Transglutaminase 3 without calcium in complex with DH patient-derived Fab DH63-B02 | ||||||||||||
Components |
| ||||||||||||
Keywords | TRANSFERASE / Transglutaminase / TGM3 / TG3 / Transglutaminase 3 / enzyme / antibody / dermatitis herpetiformis / IGHV3-9 / IGLV6-57 | ||||||||||||
Function / homology | Function and homology information protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / hair follicle morphogenesis / acyltransferase activity / keratinization / catalytic activity / keratinocyte differentiation / extrinsic component of cytoplasmic side of plasma membrane / protein modification process ...protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / hair follicle morphogenesis / acyltransferase activity / keratinization / catalytic activity / keratinocyte differentiation / extrinsic component of cytoplasmic side of plasma membrane / 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 Å | ||||||||||||
Authors | Heggelund, J.E. / Sollid, L.M. | ||||||||||||
Funding support | Norway, 3items
| ||||||||||||
Citation | Journal: Nat Commun / Year: 2023 Title: Autoantibody binding and unique enzyme-substrate intermediate conformation of human transglutaminase 3. Authors: Heggelund, J.E. / Das, S. / Stamnaes, J. / Iversen, R. / Sollid, L.M. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8oxy.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8oxy.ent.gz | 691.1 KB | Display | PDB format |
PDBx/mmJSON format | 8oxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/8oxy ftp://data.pdbj.org/pub/pdb/validation_reports/ox/8oxy | HTTPS FTP |
---|
-Related structure data
Related structure data | 8oxvC 8oxwC 8oxxC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.15151/ESRF-ES-1022934233 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 76706.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TGM3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08188 |
---|
-Antibody , 2 types, 2 molecules BC
#2: Antibody | Mass: 24112.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: IGHV3-9 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
---|---|
#3: Antibody | Mass: 23149.400 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Non-polymers , 3 types, 841 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.83 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Bicine-Tris pH 8.5, 22% Ethylene glycol, 11% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 24, 2023 |
Radiation | Monochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 2→60.43 Å / Num. obs: 88598 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.1 / Rrim(I) all: 0.151 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.92 / Num. unique obs: 4358 / CC1/2: 0.599 / Rpim(I) all: 0.812 / Rrim(I) all: 1.231 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→58.765 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.205 / SU ML: 0.134 / Cross valid method: FREE R-VALUE / ESU R: 0.163 / ESU R Free: 0.155 Details: TLS refinement. Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.537 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→58.765 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection: ALL |