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- PDB-4mf6: Crystal structure of glutathione transferase BgramDRAFT_1843 from... -

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Basic information

Entry
Database: PDB / ID: 4mf6
TitleCrystal structure of glutathione transferase BgramDRAFT_1843 from Burkholderia graminis, Target EFI-507289, with two glutathione molecules bound per one protein subunit
ComponentsGlutathione S-transferase domain
KeywordsTRANSFERASE / glutathione S-transferase / Enzyme Function Initiative / EFI / structural genomics
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / transferase activity / oxidoreductase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / GLUTATHIONE / Disulfide-bond oxidoreductase YghU
Similarity search - Component
Biological speciesBurkholderia graminis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsPatskovsky, Y. / Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. ...Patskovsky, Y. / Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of glutathione transferase BgramDRAFT_1843 from Burkholderia graminis, Target EFI-507289, with two glutathione molecules bound per one protein subunit
Authors: Patskovsky, Y. / Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, ...Authors: Patskovsky, Y. / Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C.
History
DepositionAug 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5664
Polymers28,8291
Non-polymers7373
Water6,936385
1
A: Glutathione S-transferase domain
hetero molecules

A: Glutathione S-transferase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1318
Polymers57,6582
Non-polymers1,4746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area7310 Å2
ΔGint-44 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.175, 84.175, 78.597
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-509-

HOH

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Components

#1: Protein Glutathione S-transferase domain /


Mass: 28828.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia graminis (bacteria) / Strain: C4D1M / Gene: BgramDRAFT_1843 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1FXZ2, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 0.1 M Tris-HCl, pH 8.5, 1.4 M ammonium tartrate dibasic, cryoprotectant: 20% ethylene glycol, VAPOR DIFFUSION, ...Details: protein in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 0.1 M Tris-HCl, pH 8.5, 1.4 M ammonium tartrate dibasic, cryoprotectant: 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 16, 2013 / Details: mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 88463 / % possible obs: 100 % / Observed criterion σ(I): -5 / Redundancy: 13.6 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 6.3
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IKH

4ikh


Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.874 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13111 2670 3 %RANDOM
Rwork0.11216 ---
obs0.11273 85711 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.361 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0 Å2
2--0.09 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 49 385 2335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192038
X-RAY DIFFRACTIONr_bond_other_d0.0010.021960
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9992776
X-RAY DIFFRACTIONr_angle_other_deg0.86134479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.415249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07324.10595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.70315321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0161513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212345
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02478
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_it4.4361.217972
X-RAY DIFFRACTIONr_mcbond_other4.1011.205971
X-RAY DIFFRACTIONr_mcangle_it4.031.8141217
X-RAY DIFFRACTIONr_mcangle_other4.4781.8251218
X-RAY DIFFRACTIONr_scbond_it7.4661.5271066
X-RAY DIFFRACTIONr_scbond_other7.4621.5291067
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1892.1561556
X-RAY DIFFRACTIONr_long_range_B_refined8.0466.5572796
X-RAY DIFFRACTIONr_long_range_B_other8.0456.562797
X-RAY DIFFRACTIONr_rigid_bond_restr11.23733998
X-RAY DIFFRACTIONr_sphericity_free51.016356
X-RAY DIFFRACTIONr_sphericity_bonded16.84834274
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 198 -
Rwork0.239 6244 -
obs--100 %

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