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- PDB-1kv3: HUMAN TISSUE TRANSGLUTAMINASE IN GDP BOUND FORM -

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Basic information

Entry
Database: PDB / ID: 1kv3
TitleHUMAN TISSUE TRANSGLUTAMINASE IN GDP BOUND FORM
ComponentsProtein-glutamine gamma-glutamyltransferaseTransglutaminase
KeywordsTRANSFERASE / tissue transglutaminase / GTP binding protein / crystallography
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
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. ...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
GUANOSINE-5'-DIPHOSPHATE / Protein-glutamine gamma-glutamyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiu, S. / Cerione, R.A. / Clardy, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structural basis for the guanine nucleotide-binding activity of tissue transglutaminase and its regulation of transamidation activity.
Authors: Liu, S. / Cerione, R.A. / Clardy, J.
History
DepositionJan 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Remark 999SEQUENCE According to Swissprot entry P21980, residues 51, 186, 224, 533 and 655 are in conflict. ...SEQUENCE According to Swissprot entry P21980, residues 51, 186, 224, 533 and 655 are in conflict. Residue 51 can be either GLU or GLN, Residue 186 GLU or GLN, residue 224 either VAL or GLY, residue 533 either ASN or THR, and residue 655 can be either LEU or VAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-glutamine gamma-glutamyltransferase
B: Protein-glutamine gamma-glutamyltransferase
C: Protein-glutamine gamma-glutamyltransferase
D: Protein-glutamine gamma-glutamyltransferase
E: Protein-glutamine gamma-glutamyltransferase
F: Protein-glutamine gamma-glutamyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,70912
Polymers464,0506
Non-polymers2,6596
Water7,710428
1
A: Protein-glutamine gamma-glutamyltransferase
C: Protein-glutamine gamma-glutamyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,5704
Polymers154,6832
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein-glutamine gamma-glutamyltransferase
F: Protein-glutamine gamma-glutamyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,5704
Polymers154,6832
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Protein-glutamine gamma-glutamyltransferase
E: Protein-glutamine gamma-glutamyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,5704
Polymers154,6832
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.479, 168.797, 238.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 77341.602 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGM2 / Plasmid: PET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P21980, protein-glutamine gamma-glutamyltransferase
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 50 mM MES, pH 6.6, 200 mM NaCl, 50 mM MgCl2, 6-8% PEG3350 and 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
220 mMHEPES1droppH7.0
31 mMEDTA/EGTA1drop
45 mMdithiothreitol1drop
520 %(v/v)glycerol1drop
650 mMMES1reservoirpH6.6
7200 mM1reservoirNaCl
850 mM1reservoirMgCl2
96-8 %PEG33501reservoir
105 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 29, 2000 / Details: mirros
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→52 Å / Num. all: 131998 / Num. obs: 124870 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 64.6 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 4 % / Rmerge(I) obs: 0.47 / Num. unique all: 18358 / Rsym value: 0.47 / % possible all: 88.8
Reflection
*PLUS
Lowest resolution: 51.8 Å / Num. measured all: 1141553
Reflection shell
*PLUS
% possible obs: 88.8 % / Rmerge(I) obs: 0.47

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: factor XIIIa, PDB entry 1GGU

1ggu


Resolution: 2.8→51.79 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3021702.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Non-crystallographic symmetry restrain used on 6 copies of molecules in the asymmetric unit
RfactorNum. reflection% reflectionSelection details
Rfree0.272 6267 5 %RANDOM
Rwork0.233 ---
all0.233 131998 --
obs0.233 124870 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.1343 Å2 / ksol: 0.271762 e/Å3
Displacement parametersBiso mean: 57.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å20 Å20 Å2
2---11.78 Å20 Å2
3---9.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.8→51.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30870 0 168 428 31466
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d1.49
X-RAY DIFFRACTIONc_mcbond_it2.491.5
X-RAY DIFFRACTIONc_mcangle_it4.092
X-RAY DIFFRACTIONc_scbond_it6.272
X-RAY DIFFRACTIONc_scangle_it8.452.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.401 949 4.9 %
Rwork0.36 18358 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GDP.PARGDP.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.49
LS refinement shell
*PLUS
Rfactor Rwork: 0.36

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