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- PDB-6g4h: Crystal structure of the periplasmic domain of TgpA from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 6g4h
TitleCrystal structure of the periplasmic domain of TgpA from Pseudomonas aeruginosa bound to ethylmercury
ComponentsProtein-glutamine gamma-glutamyltransferase
KeywordsTRANSFERASE / essential bacterial protein
Function / homology
Function and homology information


protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / plasma membrane
Similarity search - Function
Protein-glutamine gamma-glutamyltransferase TgpA, N-terminal / Domain of unknown function DUF4129 / : / TgpA N-terminal domain / Domain of unknown function (DUF4129) / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
ETHYL MERCURY ION / PHOSPHATE ION / Protein-glutamine gamma-glutamyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsMilani, M. / Mastrangelo, E. / Uruburu, M.
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structural and functional characterization of TgpA, a critical protein for the viability of Pseudomonas aeruginosa.
Authors: Uruburu, M. / Mastrangelo, E. / Bolognesi, M. / Ferrara, S. / Bertoni, G. / Milani, M.
History
DepositionMar 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)39,0526
Polymers38,4421
Non-polymers6105
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-26 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.470, 72.470, 157.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-899-

HOH

21A-914-

HOH

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Components

#1: Protein Protein-glutamine gamma-glutamyltransferase / Transglutaminase protein A / TGase A


Mass: 38442.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: protein TAG: MGSDKIHHHHHHHHHHGV / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: tgpA, PA2873 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HZX3, protein-glutamine gamma-glutamyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 293 K / Method: batch mode / Details: Ammonium dihydrogen phosphate 0.7 M, pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.00775 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00775 Å / Relative weight: 1
ReflectionResolution: 1.8→48.7 Å / Num. obs: 529624 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 8.4
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 1.14

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementResolution: 1.8→48.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.141 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.091 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18716 1988 5 %RANDOM
Rwork0.15644 ---
obs0.15796 37765 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.031 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.8→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 23 316 2590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192383
X-RAY DIFFRACTIONr_bond_other_d0.0010.022113
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.943255
X-RAY DIFFRACTIONr_angle_other_deg0.8434881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9375290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17622.615130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90415363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2041528
X-RAY DIFFRACTIONr_chiral_restr0.1060.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212701
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02551
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.482.431124
X-RAY DIFFRACTIONr_mcbond_other2.4772.4281123
X-RAY DIFFRACTIONr_mcangle_it3.4173.6241405
X-RAY DIFFRACTIONr_mcangle_other3.4183.6271406
X-RAY DIFFRACTIONr_scbond_it4.7162.9511259
X-RAY DIFFRACTIONr_scbond_other4.6591259
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.81228.8881844
X-RAY DIFFRACTIONr_long_range_B_refined8.56130.5242777
X-RAY DIFFRACTIONr_long_range_B_other8.00629.3872668
X-RAY DIFFRACTIONr_rigid_bond_restr88.32532
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded89.8953
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 143 -
Rwork0.315 2710 -
obs--99.1 %

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