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Basic information

Entry
Database: PDB / ID: 1nud
TitleRole of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 calciums, active form)
ComponentsProtein-glutamine glutamyltransferase E
KeywordsTRANSFERASE / 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 / 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
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
BROMIDE ION / Protein-glutamine gamma-glutamyltransferase E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAhvazi, 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
DepositionJan 31, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 295 NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE ... NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH ATOMS ARE NOT FOUND IN THIS ENTRY. APPLIED TO TRANSFORMED TO TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD SSS M 1 A 1 .. 692 B 1 .. 692 0.408 WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS REMARK: THE MATRIX TRANSFORMS CA ONLY.
Remark 400COMPOUND THE ENZYME WAS PROTEOLYZED WITH DISPASE I FOR ACTIVATION.
Remark 999SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-glutamine glutamyltransferase E
B: Protein-glutamine glutamyltransferase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,58425
Polymers153,3412
Non-polymers1,24323
Water7,170398
1
A: Protein-glutamine glutamyltransferase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,25212
Polymers76,6711
Non-polymers58211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein-glutamine glutamyltransferase E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,33213
Polymers76,6711
Non-polymers66212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.54, 115.37, 121.39
Angle α, β, γ (deg.)90, 92.66, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, 0.00023, -0.00133), (-0.0002, 0.99964, 0.02673), (0.00134, -0.02673, 0.99964)
Vector: 54.8172, 3.91267, 60.96515)

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Components

#1: Protein Protein-glutamine glutamyltransferase E / TGase E / TGE / TGE / Transglutaminase 3


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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 4% (w/v) Peg 20K, 100 mM Tris-HCl (pH 8.5) , VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 mMbeta-octylglucoside1drop
320 mMTris-HCl1droppH8.0
41 mMEDTA1drop
5125 mg/ml1dropNaCl
617 mg/mlprotein1drop
74 %(w/v)PEG200001reservoir
8100 mMTris-HCl1reservoirpH8.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONNSLS X9B20.92
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IIC1IMAGE PLATEJun 7, 2000mirrors
ADSC QUANTUM 42CCDJun 7, 2000mirrors
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.921
ReflectionResolution: 2.7→20 Å / Num. all: 41052 / Num. obs: 41052 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 23.8 Å2 / Net I/σ(I): 8.9
Reflection shellResolution: 2.7→2.87 Å / % possible all: 88.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 409995
Reflection shell
*PLUS
Lowest resolution: 2.8 Å / % possible obs: 88.4 % / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1L9N

1l9n


Resolution: 2.7→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: NCS two fold averaging was employed during refinement
RfactorNum. reflectionSelection details
Rfree0.265 3958 RANDOM
Rwork0.199 --
all-41052 -
obs-39296 -
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.67 Å20 Å20.83 Å2
2--1.08 Å20 Å2
3---3.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10500 0 23 398 10921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it0.47
X-RAY DIFFRACTIONc_mcangle_it0.87
X-RAY DIFFRACTIONc_scbond_it0.52
X-RAY DIFFRACTIONc_scangle_it0.86
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.369 571 -
Rwork0.282 --
obs-5314 9.7 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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