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- PDB-1l9m: Three-dimensional structure of the human transglutaminase 3 enzym... -

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Basic information

Entry
Database: PDB / ID: 1l9m
TitleThree-dimensional structure of the human transglutaminase 3 enzyme: binding of calcium ions change structure for activation
ComponentsProtein-glutamine glutamyltransferase E3
KeywordsTRANSFERASE / Activation / Calcium binding / transglutaminase
Function / homology
Function and homology information


protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / extrinsic component of cytoplasmic side of plasma membrane / hair follicle morphogenesis / acyltransferase activity / keratinization / catalytic activity / keratinocyte differentiation / protein modification process ...protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / peptide cross-linking / extrinsic component of cytoplasmic side of plasma membrane / hair follicle morphogenesis / acyltransferase activity / keratinization / catalytic activity / keratinocyte differentiation / 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 ...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 / Immunoglobulin-like fold / Immunoglobulins / 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: 2.1 Å
AuthorsAhvazi, B.
Citation
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.
#1: Journal: FEBS Lett. / Year: 1998
Title: Two non-proline cis peptide bonds may be important for factor XIII function
Authors: Yee, V.C. / Pedersen, L.C. / Le Trong, I. / Bishop, P.D. / Stenkamp, R.E. / Teller, D.C.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Three-dimensional structure of a transglutaminase: human blood coagulation factor XII
Authors: Weiss, M.S. / Metzner, H.J. / Hilgenfeld, R.
History
DepositionMar 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / 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_database_remark.text / _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.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 999 The following residues are noted as conflicts in the Swiss-Prot database: K12T, K561R, G654R. ... The following residues are noted as conflicts in the Swiss-Prot database: K12T, K561R, G654R. According to the author, residue 250 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

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Assembly

Deposited unit
A: Protein-glutamine glutamyltransferase E3
B: Protein-glutamine glutamyltransferase E3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,6528
Polymers153,3412
Non-polymers3116
Water16,232901
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.709, 67.515, 116.208
Angle α, β, γ (deg.)97.24, 90.15, 98.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein-glutamine glutamyltransferase E3 / Transglutaminase 3 / TGM3 / TGASE E3


Mass: 76670.500 Da / Num. of mol.: 2 / Mutation: F264L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Foreskin / Gene: TGM3 / Plasmid: Bac-N-Blue, Invitrogen / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): baculovirus system
References: UniProt: Q08188, protein-glutamine gamma-glutamyltransferase
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 901 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.51 %
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: 15 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 mMbeta-octylglucoside1drop
220 mMTris-HCl1droppH8.0
31 mMEDTA1drop
4125 mM1dropNaCl
517 mg/mlprotein1drop
64 %(w/v)PEG200001reservoir
7100 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 PLATEAug 15, 1999mirrors
ADSC QUANTUM 42CCDJul 26, 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: 2.1→20 Å / Num. obs: 75013 / % possible obs: 93 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.2 Å2 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→20 Å / % possible all: 93
Reflection
*PLUS
Highest resolution: 2.2 Å / % possible obs: 94.6 % / Num. measured all: 521626
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / % possible obs: 93 % / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GGT

1ggt


Resolution: 2.1→20 Å / 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
Rfree0.225 7350 RANDOM
Rwork0.182 --
all0.248 72799 -
obs0.296 72799 -
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.03 Å2-2.78 Å2-0.56 Å2
2--6.12 Å21.32 Å2
3----3.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10580 0 6 901 11487
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d25.54
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it0.86
X-RAY DIFFRACTIONc_mcangle_it1.48
X-RAY DIFFRACTIONc_scbond_it1.19
X-RAY DIFFRACTIONc_scangle_it1.79
LS refinement shellResolution: 2.1→2.34 Å / Rfactor Rfree error: 0.009
RfactorNum. reflection% reflection
Rfree0.296 1055 -
Rwork0.248 --
obs-9838 9.7 %
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.182 / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.54
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor obs: 0.248

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