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- PDB-4uss: Populus trichocarpa glutathione transferase X1-1 (GHR1), complexe... -

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Basic information

Entry
Database: PDB / ID: 4uss
TitlePopulus trichocarpa glutathione transferase X1-1 (GHR1), complexed with glutathione
ComponentsGLUTATHIONYL HYDROQUINONE REDUCTASE
KeywordsTRANSFERASE / CLASS XI / POPLAR / PLASTIDS
Function / homology
Function and homology information


Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutaredoxin / Glutaredoxin / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / PHOSPHATE ION / :
Similarity search - Component
Biological speciesPOPULUS TRICHOCARPA (black cottonwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLallement, P.A. / Meux, E. / Gualberto, J.M. / Dumaracay, S. / Favier, F. / Didierjean, C. / Saul, F. / Haouz, A. / Morel-Rouhier, M. / Gelhaye, E. ...Lallement, P.A. / Meux, E. / Gualberto, J.M. / Dumaracay, S. / Favier, F. / Didierjean, C. / Saul, F. / Haouz, A. / Morel-Rouhier, M. / Gelhaye, E. / Rouhier, N. / Hecker, A.
CitationJournal: FEBS Lett. / Year: 2015
Title: Glutathionyl-Hydroquinone Reductases from Poplar are Plastidial Proteins that Deglutathionylate Both Reduced and Oxidized Glutathionylated Quinones.
Authors: Lallement, P. / Meux, E. / Gualberto, J.M. / Dumarcay, S. / Favier, F. / Didierjean, C. / Saul, F. / Haouz, A. / Morel-Rouhier, M. / Gelhaye, E. / Rouhier, N. / Hecker, A.
History
DepositionJul 13, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
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 / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTATHIONYL HYDROQUINONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6784
Polymers37,1811
Non-polymers4973
Water1,26170
1
A: GLUTATHIONYL HYDROQUINONE REDUCTASE
hetero molecules

A: GLUTATHIONYL HYDROQUINONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3568
Polymers74,3622
Non-polymers9956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4570 Å2
ΔGint-45.4 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.530, 92.409, 86.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein GLUTATHIONYL HYDROQUINONE REDUCTASE


Mass: 37180.754 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-359
Source method: isolated from a genetically manipulated source
Details: THE EXPRESSED PROTEIN IS DEVOID OF THE FIRST 34 AMINO ACIDS.
Source: (gene. exp.) POPULUS TRICHOCARPA (black cottonwood) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B9ICN7, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDISCREPANCIES IN SEQUENCE ARE DUE TO POLYMORPHISM. AUTHORS HAVE CLARIFIED THAT DISCREPANCIES IN ...DISCREPANCIES IN SEQUENCE ARE DUE TO POLYMORPHISM. AUTHORS HAVE CLARIFIED THAT DISCREPANCIES IN SEQUENCE ARE DUE TO POLYMORPHISM (RESIDUES 105, 175, 181, AND 185)

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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: 1.97 Å3/Da / Density % sol: 37.64 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.82656
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2011 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 2.5→19.53 Å / Num. obs: 10702 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 35.73 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 12.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3 / % possible all: 82.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PPU

3ppu


Resolution: 2.5→19.525 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 548 5.1 %
Rwork0.1834 --
obs0.1862 10702 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 30 70 2579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032574
X-RAY DIFFRACTIONf_angle_d0.6683491
X-RAY DIFFRACTIONf_dihedral_angle_d12.561949
X-RAY DIFFRACTIONf_chiral_restr0.029363
X-RAY DIFFRACTIONf_plane_restr0.002454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.75110.31081260.23462479X-RAY DIFFRACTION100
2.7511-3.14780.31441250.23622502X-RAY DIFFRACTION100
3.1478-3.96040.24781400.18182534X-RAY DIFFRACTION100
3.9604-19.52590.17661570.14782639X-RAY DIFFRACTION100

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