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- PDB-4mf7: Crystal structure of glutathione transferase BBTA-3750 from Brady... -

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Basic information

Entry
Database: PDB / ID: 4mf7
TitleCrystal structure of glutathione transferase BBTA-3750 from Bradyrhizobium sp., Target EFI-507290
Componentsglutathione S-transferase enzyme with thioredoxin-like domain
KeywordsTRANSFERASE / glutathione S-transferase / Enzyme Function Initiative / EFI / structural genomics
Function / homology
Function and homology information


transferase 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
Putative glutathione S-transferase enzyme with thioredoxin-like domain
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 BBTA-3750 from Bradyrhizobium sp., Target EFI-507290
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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glutathione S-transferase enzyme with thioredoxin-like domain


Theoretical massNumber of molelcules
Total (without water)29,0381
Polymers29,0381
Non-polymers00
Water3,117173
1
A: glutathione S-transferase enzyme with thioredoxin-like domain

A: glutathione S-transferase enzyme with thioredoxin-like domain


Theoretical massNumber of molelcules
Total (without water)58,0762
Polymers58,0762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2230 Å2
ΔGint-15 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.526, 88.951, 78.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein glutathione S-transferase enzyme with thioredoxin-like domain


Mass: 29038.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium sp. (bacteria) / Strain: BTAi1 / ATCC BAA-1182 / Gene: BBta_3750 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5EI34, glutathione transferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: protein in 10 MM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 0.2 M potassium nitrate, pH 6.9, 20% PEG3350, cryoprotectant: 20% diethylene glycol, VAPOR DIFFUSION, SITTING ...Details: protein in 10 MM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, reservoir: 0.2 M potassium nitrate, pH 6.9, 20% PEG3350, cryoprotectant: 20% diethylene 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: 1.8→50 Å / Num. obs: 25702 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 7.4 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 13.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.8 / % 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: 1.8→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.599 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21858 829 3.2 %RANDOM
Rwork0.17693 ---
obs0.17821 24850 99.85 %-
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: 40.306 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2--1.29 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 0 173 1800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191685
X-RAY DIFFRACTIONr_bond_other_d0.0010.021609
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9712294
X-RAY DIFFRACTIONr_angle_other_deg0.83833703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.835205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81923.63677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69215270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0331512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
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_it7.64.908820
X-RAY DIFFRACTIONr_mcbond_other7.5964.908821
X-RAY DIFFRACTIONr_mcangle_it7.6218.1851022
X-RAY DIFFRACTIONr_mcangle_other7.6188.1871023
X-RAY DIFFRACTIONr_scbond_it11.7965.705864
X-RAY DIFFRACTIONr_scbond_other11.8165.709861
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.4099.1761272
X-RAY DIFFRACTIONr_long_range_B_refined12.52523.182035
X-RAY DIFFRACTIONr_long_range_B_other12.67122.9171962
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 69 -
Rwork0.272 1799 -
obs--100 %

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