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- PDB-6tho: Acylintermediate of glutathione and the mature primitive phytoche... -

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Basic information

Entry
Database: PDB / ID: 6tho
TitleAcylintermediate of glutathione and the mature primitive phytochelatin synthase Alr0975 from Nostoc PCC 7120 at atomic resolution.
ComponentsAlr0975 protein
KeywordsTRANSFERASE / glutathione / phytochelatin / detoxification / chelating heavy atoms
Function / homology
Function and homology information


glutathione gamma-glutamylcysteinyltransferase / glutathione gamma-glutamylcysteinyltransferase activity / phytochelatin biosynthetic process / response to metal ion / metal ion binding
Similarity search - Function
Phytochelatin synthase, N-terminal catalytic domain / Phytochelatin synthase, N-terminal domain superfamily / Phytochelatin synthase / Phytochelatin synthase / Phytochelatin synthase (PCS) domain profile. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
OXIDIZED GLUTATHIONE DISULFIDE / glutathione gamma-glutamylcysteinyltransferase
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsFeiler, C.G. / Blankenfeldt, W.
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Structural and Biophysical Analysis of the Phytochelatin-Synthase-Like Enzyme from Nostoc sp. Shows That Its Protease Activity is Sensitive to the Redox State of the Substrate.
Authors: Gisdon, F.J. / Feiler, C.G. / Kempf, O. / Foerster, J.M. / Haiss, J. / Blankenfeldt, W. / Ullmann, G.M. / Bombarda, E.
History
DepositionNov 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alr0975 protein
B: Alr0975 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5208
Polymers50,1352
Non-polymers1,3866
Water12,971720
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-42 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.283, 57.956, 139.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Alr0975 protein / Primitive phytochelatin synthase


Mass: 25067.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Gene: alr0975, alr0975 / Plasmid: p10$ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YY76
#2: Chemical ChemComp-GDS / OXIDIZED GLUTATHIONE DISULFIDE


Mass: 612.631 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32N6O12S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 720 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 16.5% PEG 8000, 0.1M MES pH 5.5, 0.18 M CaAc, 5 mM glutathione cryoprotectant 20% glycerol
PH range: 5-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.09→29.21 Å / Num. obs: 164591 / % possible obs: 98.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 8.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05585 / Rpim(I) all: 0.03381 / Rrim(I) all: 0.06559 / Net I/σ(I): 12.06
Reflection shellResolution: 1.09→1.129 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4272 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 55829 / CC1/2: 0.815 / Rpim(I) all: 0.2616 / Rrim(I) all: 0.5034 / % possible all: 99.33

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TH5

6th5


Resolution: 1.09→29.21 Å / SU ML: 0.0786 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.4459
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1483 8269 5.02 %
Rwork0.1182 156318 -
obs0.1197 164587 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.98 Å2
Refinement stepCycle: LAST / Resolution: 1.09→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 74 720 4278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074365
X-RAY DIFFRACTIONf_angle_d1.04196011
X-RAY DIFFRACTIONf_chiral_restr0.0807664
X-RAY DIFFRACTIONf_plane_restr0.0073798
X-RAY DIFFRACTIONf_dihedral_angle_d29.2233664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.10.20482830.19995207X-RAY DIFFRACTION99.12
1.1-1.120.21642530.18875221X-RAY DIFFRACTION99.45
1.12-1.130.2052620.17485206X-RAY DIFFRACTION99.44
1.13-1.140.19232850.16655193X-RAY DIFFRACTION99.56
1.14-1.160.1672780.15385182X-RAY DIFFRACTION99.62
1.16-1.170.17452570.14515259X-RAY DIFFRACTION99.67
1.17-1.190.16222630.1415193X-RAY DIFFRACTION99.42
1.19-1.210.1682880.13875225X-RAY DIFFRACTION99.67
1.21-1.230.17963000.13855184X-RAY DIFFRACTION99.51
1.23-1.250.1662530.13315227X-RAY DIFFRACTION99.53
1.25-1.270.15442570.12895267X-RAY DIFFRACTION99.53
1.27-1.290.16282930.12775176X-RAY DIFFRACTION99.33
1.29-1.320.16142640.1235239X-RAY DIFFRACTION99.64
1.32-1.340.15082630.1225232X-RAY DIFFRACTION99.46
1.34-1.370.14312820.11715203X-RAY DIFFRACTION99.37
1.37-1.410.15472930.11385206X-RAY DIFFRACTION99.3
1.41-1.440.14332700.11375198X-RAY DIFFRACTION99.11
1.44-1.480.14252930.11075229X-RAY DIFFRACTION99.33
1.48-1.520.14772810.1075239X-RAY DIFFRACTION99.08
1.52-1.570.14412630.10635203X-RAY DIFFRACTION98.5
1.57-1.630.14332870.10695167X-RAY DIFFRACTION98.7
1.63-1.690.12622700.1065232X-RAY DIFFRACTION98.21
1.69-1.770.12952790.10625185X-RAY DIFFRACTION97.96
1.77-1.860.12512760.10535133X-RAY DIFFRACTION97.28
1.86-1.980.13552800.10595156X-RAY DIFFRACTION96.93
1.98-2.130.13722590.10565124X-RAY DIFFRACTION95.99
2.13-2.350.12472810.10495131X-RAY DIFFRACTION95.84
2.35-2.690.13562760.11025158X-RAY DIFFRACTION96.16
2.69-3.390.16312660.11225248X-RAY DIFFRACTION96.43
3.39-29.210.15063140.12175495X-RAY DIFFRACTION97.42

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