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- PDB-6ghf: Crystal structure of a GST variant -

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Basic information

Entry
Database: PDB / ID: 6ghf
TitleCrystal structure of a GST variant
ComponentsPvGmGSTUG
KeywordsBIOSYNTHETIC PROTEIN / gene shuffling / transferase
Function / homologyGlutathione 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
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsPapageorgiou, A.C. / Chronopoulou, E.G. / Labrou, N.E.
CitationJournal: Front Plant Sci / Year: 2018
Title: Expanding the Plant GSTome Through Directed Evolution: DNA Shuffling for the Generation of New Synthetic Enzymes With Engineered Catalytic and Binding Properties.
Authors: Chronopoulou, E.G. / Papageorgiou, A.C. / Ataya, F. / Nianiou-Obeidat, I. / Madesis, P. / Labrou, N.E.
History
DepositionMay 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: PvGmGSTUG
A: PvGmGSTUG


Theoretical massNumber of molelcules
Total (without water)52,2482
Polymers52,2482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-17 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.000, 51.000, 227.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 6 - 212 / Label seq-ID: 6 - 212

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

#1: Protein PvGmGSTUG


Mass: 26124.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The gene expressing PvGmGSTUG was constructed by gene shuffling of a Phaseolus vulgaris GST and a Glycine max GST.
Source: (gene. exp.) synthetic construct (others) / Gene: Synthetic / Production host: Escherichia coli (E. coli)

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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: 2.83 Å3/Da / Density % sol: 56.56 % / Description: Rods
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000 20% (w/v), Na succinate 0.2 M, Hepes-NaOH 0.1 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 3.5→56.87 Å / Num. obs: 7132 / % possible obs: 98.6 % / Redundancy: 4.8 % / CC1/2: 0.998 / Rrim(I) all: 0.099 / Net I/σ(I): 8.8
Reflection shellResolution: 3.5→3.6 Å / Mean I/σ(I) obs: 1.3 / CC1/2: 0.656 / Rrim(I) all: 1.38 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J2F

4j2f


Resolution: 3.52→56.87 Å / Cor.coef. Fo:Fc: 0.843 / Cor.coef. Fo:Fc free: 0.818 / SU B: 56.206 / SU ML: 0.888 / Cross valid method: THROUGHOUT / ESU R Free: 0.893 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33325 709 10 %RANDOM
Rwork0.29536 ---
obs0.29935 6401 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 80.914 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-0 Å2
2--0.64 Å2-0 Å2
3----1.28 Å2
Refinement stepCycle: 1 / Resolution: 3.52→56.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 0 0 3431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193523
X-RAY DIFFRACTIONr_bond_other_d0.0030.023382
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9684762
X-RAY DIFFRACTIONr_angle_other_deg1.17537828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.495416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85624.233163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33915635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4131516
X-RAY DIFFRACTIONr_chiral_restr0.0970.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213852
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02788
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_it6.3918.0951670
X-RAY DIFFRACTIONr_mcbond_other6.3928.0961669
X-RAY DIFFRACTIONr_mcangle_it10.7312.1242084
X-RAY DIFFRACTIONr_mcangle_other10.72812.1222085
X-RAY DIFFRACTIONr_scbond_it5.0268.2581853
X-RAY DIFFRACTIONr_scbond_other5.0258.2571854
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.79912.2292679
X-RAY DIFFRACTIONr_long_range_B_refined22.16218698
X-RAY DIFFRACTIONr_long_range_B_other22.16118699
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11372 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.21 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 3.52→3.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 54 -
Rwork0.309 498 -
obs--98.75 %

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