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- PDB-1g0d: CRYSTAL STRUCTURE OF RED SEA BREAM TRANSGLUTAMINASE -

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Basic information

Entry
Database: PDB / ID: 1g0d
TitleCRYSTAL STRUCTURE OF RED SEA BREAM TRANSGLUTAMINASE
ComponentsPROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE
KeywordsTRANSFERASE / tissue transglutaminase / acyltransferase
Function / homology
Function and homology information


protein deamination / histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / cellular response to serotonin / regulation of apoptotic cell clearance / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein-glutamine gamma-glutamyltransferase ...protein deamination / histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / cellular response to serotonin / regulation of apoptotic cell clearance / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / cellular response to dopamine / positive regulation of small GTPase mediated signal transduction / Hydrolases; Acting on peptide bonds (peptidases) / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of GTPase activity / bone development / protein homooligomerization / peptidase activity / nervous system development / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of apoptotic process / positive regulation of apoptotic process / calcium ion binding / chromatin / GTP binding / mitochondrion / proteolysis / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / : / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain ...Coagulation Factor XIII; Chain A, domain 2 / Transglutaminase-like / : / Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Transglutaminase-like superfamily / Papain-like cysteine peptidase superfamily / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein-glutamine gamma-glutamyltransferase 2
Similarity search - Component
Biological speciesPagrus major (red seabream)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsNoguchi, K. / Ishikawa, K. / Yokoyama, K. / Ohtsuka, T. / Nio, N. / Suzuki, E.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of red sea bream transglutaminase.
Authors: Noguchi, K. / Ishikawa, K. / Yokoyama, K.i. / Ohtsuka, T. / Nio, N. / Suzuki, E.
#1: Journal: Biosci.Biotechnol.Biochem. / Year: 1998
Title: Overproduction of DnaJ in Escherichia coli Improves in Vivo Solubility of the Recombinant Fish-derived Transglutaminase
Authors: Yokoyama, K. / Kikuchi, Y. / Yasueda, H.
#2: Journal: Eur.J.Biochem. / Year: 1995
Title: Tissue-type transglutaminase from red sea bream (Pagrus major)
Authors: Yasueda, H. / Nakanishi, K. / Kumazawa, Y. / Nagase, K. / Motoki, M. / Matsui, H.
History
DepositionOct 6, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4172
Polymers78,3211
Non-polymers961
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.800, 97.800, 455.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE


Mass: 78320.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pagrus major (red seabream) / Tissue: LIVER / Plasmid: PTTNCO / Production host: Escherichia coli (E. coli)
References: UniProt: P52181, protein-glutamine gamma-glutamyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulfate, PEG6000, Hepes, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.8 Mammonium sulfate1reservoir
21 %PEG60001reservoir
30.1 MHEPES1reservoir
45 mMdithiothreitol1reservoir
514 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Feb 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 45422 / Num. obs: 39366 / % possible obs: 86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.62 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 6.6
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.162 / % possible all: 61.4

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR98.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3936 -RANDOM
Rwork0.2 ---
all-39366 --
obs-39366 86 %-
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5283 0 5 383 5671
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg1.99
X-RAY DIFFRACTIONx_dihedral_angle_d28.525
X-RAY DIFFRACTIONx_improper_angle_d1.033
Software
*PLUS
Name: X-PLOR / Version: 98.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Num. reflection obs: 37856 / σ(F): 2 / Rfactor obs: 0.196 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.454
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.525
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.033

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