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- PDB-6kzb: Transglutaminase2 complexed with calcium -

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Basic information

Entry
Database: PDB / ID: 6kzb
TitleTransglutaminase2 complexed with calcium
ComponentsProtein-glutamine gamma-glutamyltransferase 2Transglutaminase
KeywordsTRANSFERASE / Protein-glutamine gamma-glutamyltransferase 2
Function / homology
Function and homology information


histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / cellular response to serotonin / regulation of apoptotic cell clearance / protein deamination / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein-glutamine gamma-glutamyltransferase ...histone serotonyltransferase activity / histone dopaminyltransferase activity / peptide noradrenalinyltransferase activity / peptide histaminyltransferase activity / cellular response to serotonin / regulation of apoptotic cell clearance / protein deamination / protein-glutamine glutaminase activity / protein-glutamine glutaminase / protein-glutamine gamma-glutamyltransferase / positive regulation of mitochondrial calcium ion concentration / salivary gland cavitation / protein-glutamine gamma-glutamyltransferase activity / negative regulation of endoplasmic reticulum calcium ion concentration / dopamine secretion / peptide cross-linking / branching involved in salivary gland morphogenesis / cellular response to dopamine / positive regulation of small GTPase mediated signal transduction / Hydrolases; Acting on peptide bonds (peptidases) / apoptotic cell clearance / cellular response to cocaine / positive regulation of neurogenesis / positive regulation of cell adhesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / extracellular matrix / protein homooligomerization / bone development / positive regulation of GTPase activity / nucleosome / gene expression / phospholipase C-activating G protein-coupled receptor signaling pathway / peptidase activity / collagen-containing extracellular matrix / regulation of apoptotic process / positive regulation of apoptotic process / focal adhesion / calcium ion binding / chromatin / GTP binding / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / proteolysis / extracellular exosome / nucleus / plasma membrane / cytosol
Similarity search - Function
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, 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Protein-glutamine gamma-glutamyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsPark, H.H. / Kim, C.M.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2020
Title: Competitive Binding of Magnesium to Calcium Binding Sites Reciprocally Regulates Transamidase and GTP Hydrolysis Activity of Transglutaminase 2.
Authors: Jeong, E.M. / Lee, K.B. / Kim, G.E. / Kim, C.M. / Lee, J.H. / Kim, H.J. / Shin, J.W. / Kwon, M.A. / Park, H.H. / Kim, I.G.
History
DepositionSep 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-glutamine gamma-glutamyltransferase 2
B: Protein-glutamine gamma-glutamyltransferase 2
C: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,80812
Polymers232,2383
Non-polymers1,5709
Water0
1
A: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules

A: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,8728
Polymers154,8252
Non-polymers1,0476
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4010 Å2
ΔGint-47 kcal/mol
Surface area53570 Å2
MethodPISA
2
B: Protein-glutamine gamma-glutamyltransferase 2
C: Protein-glutamine gamma-glutamyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,8728
Polymers154,8252
Non-polymers1,0476
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-44 kcal/mol
Surface area51760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.080, 216.307, 166.263
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein-glutamine gamma-glutamyltransferase 2 / Transglutaminase / Tissue transglutaminase / Transglutaminase C / TGase C / Transglutaminase H / TGase H / ...Tissue transglutaminase / Transglutaminase C / TGase C / Transglutaminase H / TGase H / Transglutaminase-2 / TGase-2


Mass: 77412.680 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGM2 / Production host: Escherichia coli (E. coli)
References: UniProt: P21980, protein-glutamine gamma-glutamyltransferase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Potassium chloride, Magnesium acetate tetrahydrate, Sodium cacodylate, Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.55→42.585 Å / Num. obs: 29265 / % possible obs: 99.99 % / Redundancy: 10.9 % / Rsym value: 0.113 / Net I/σ(I): 8.95
Reflection shellResolution: 3.56→3.62 Å / Num. unique obs: 1454 / Rsym value: 0.391

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PYG

4pyg


Resolution: 3.55→42.585 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.864 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.207 / Average fsc free: 0.9057 / Average fsc work: 0.9225 / Cross valid method: FREE R-VALUE / ESU R Free: 0.714
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2619 1490 5.095 %
Rwork0.2266 27752 -
all0.228 --
obs-29242 99.595 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 60.856 Å2
Baniso -1Baniso -2Baniso -3
1-0.016 Å20 Å2-0 Å2
2---0.003 Å20 Å2
3----0.013 Å2
Refinement stepCycle: LAST / Resolution: 3.55→42.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15665 0 90 0 15755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01316095
X-RAY DIFFRACTIONr_bond_other_d0.0360.01714619
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.64821886
X-RAY DIFFRACTIONr_angle_other_deg2.3111.57533862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.60351989
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49922.419860
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.582152620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1715109
X-RAY DIFFRACTIONr_chiral_restr0.0980.22068
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218074
X-RAY DIFFRACTIONr_gen_planes_other0.0290.023393
X-RAY DIFFRACTIONr_nbd_refined0.2080.23435
X-RAY DIFFRACTIONr_symmetry_nbd_other0.260.215391
X-RAY DIFFRACTIONr_nbtor_refined0.1890.27752
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.28585
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2378
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1250.235
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2510.233
X-RAY DIFFRACTIONr_nbd_other0.3360.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3080.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1930.25
X-RAY DIFFRACTIONr_mcbond_it4.4316.7288007
X-RAY DIFFRACTIONr_mcbond_other4.4316.7298006
X-RAY DIFFRACTIONr_mcangle_it6.72410.0789978
X-RAY DIFFRACTIONr_mcangle_other6.72410.0779979
X-RAY DIFFRACTIONr_scbond_it5.7996.7648088
X-RAY DIFFRACTIONr_scbond_other5.796.7628080
X-RAY DIFFRACTIONr_scangle_it7.94910.09311907
X-RAY DIFFRACTIONr_scangle_other7.93910.0911895
X-RAY DIFFRACTIONr_lrange_it8.54577.62217722
X-RAY DIFFRACTIONr_lrange_other8.54577.61117720
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.55-3.6410.3511230.28419170.28721180.8390.87796.31730.255
3.641-3.740.2971240.26119760.26321000.8650.8931000.237
3.74-3.8480.317750.25419390.25620140.8590.8961000.223
3.848-3.9650.279940.24318630.24519590.8970.90999.89790.213
3.965-4.0940.2451050.22717980.22819030.920.9261000.2
4.094-4.2370.239780.21117660.21218440.9310.9391000.188
4.237-4.3950.238780.19617050.19817830.9290.9431000.175
4.395-4.5720.209910.19716120.19817030.9490.9471000.172
4.572-4.7730.2081070.18215620.18416690.9410.9491000.161
4.773-5.0030.237810.19414900.19715710.9290.9391000.174
5.003-5.2690.229660.20814490.20915150.9270.941000.184
5.269-5.5840.281700.22613580.22914280.90.9271000.202
5.584-5.9620.291610.22413020.22713630.9110.9151000.197
5.962-6.4290.327810.25411810.25812620.880.9011000.231
6.429-7.0270.286500.2611300.26111800.8910.9221000.233
7.027-7.830.294710.2379930.24110640.8960.9251000.225
7.83-8.990.262530.2098950.2129480.9330.9431000.208
8.99-10.890.2420.2057840.2058260.9570.9561000.206
10.89-14.9210.199240.2146350.2136600.9470.94899.84850.223
14.921-42.5850.357160.3493970.354290.9290.89996.27040.363

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