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- PDB-6g49: Crystal structure of the periplasmic domain of TgpA from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 6g49
TitleCrystal structure of the periplasmic domain of TgpA from Pseudomonas aeruginosa
ComponentsProtein-glutamine gamma-glutamyltransferaseTransglutaminase
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
PHOSPHATE ION / Protein-glutamine gamma-glutamyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.1Sep 18, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.number_all / _reflns.number_obs ..._reflns.number_all / _reflns.number_obs / _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all
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)39,1429
Polymers38,4421
Non-polymers7008
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-48 kcal/mol
Surface area12490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.640, 71.640, 164.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein-glutamine gamma-glutamyltransferase / Transglutaminase / 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 / Gene: tgpA, PA2873 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HZX3, protein-glutamine gamma-glutamyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5 0.8 M Sodium phosphate monobasic monohydrate 0.8 M Potassium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.6→43.5 Å / Num. all: 429906 / Num. obs: 57370 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rpim(I) all: 0.032 / Rrim(I) all: 0.064 / Net I/σ(I): 17.6
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 1.66 / Num. unique obs: 4156 / CC1/2: 0.739 / Rpim(I) all: 0.682 / Rrim(I) all: 1.468

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→43.5 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19391 2864 5 %RANDOM
Rwork0.16045 ---
obs0.1621 54413 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.278 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--0.92 Å20 Å2
3----1.84 Å2
Refinement stepCycle: 1 / Resolution: 1.6→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 36 287 2645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0142613
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172199
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.6763598
X-RAY DIFFRACTIONr_angle_other_deg1.6041.6185211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.655336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30420.109183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09315419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6731535
X-RAY DIFFRACTIONr_chiral_restr0.1040.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023066
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02510
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_it2.8562.5751203
X-RAY DIFFRACTIONr_mcbond_other2.8572.5741202
X-RAY DIFFRACTIONr_mcangle_it3.7243.851515
X-RAY DIFFRACTIONr_mcangle_other3.7233.8511516
X-RAY DIFFRACTIONr_scbond_it6.2933.0911410
X-RAY DIFFRACTIONr_scbond_other5.1753.0191383
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2064.3572016
X-RAY DIFFRACTIONr_long_range_B_refined9.26132.0423087
X-RAY DIFFRACTIONr_long_range_B_other8.81231.0772994
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 208 -
Rwork0.304 3942 -
obs--100 %

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