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- PDB-4pts: Crystal structure of a glutathione transferase from Gordonia bron... -

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Basic information

Entry
Database: PDB / ID: 4pts
TitleCrystal structure of a glutathione transferase from Gordonia bronchialis DSM 43247, target EFI-507405
Componentsglutathione S-transferase
KeywordsTRANSFERASE / structural genomics / Enzyme Function Initiative / GSH
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
Glutathione S-transferase Omega/GSH / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 ...Glutathione S-transferase Omega/GSH / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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
Glutathione transferase
Similarity search - Component
Biological speciesGordonia bronchialis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsKim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. ...Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a glutathione transferase from Gordonia bronchialis DSM 43247, target EFI-507405
Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / ...Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C.
History
DepositionMar 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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_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

Downloads & links

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Assembly

Deposited unit
A: glutathione S-transferase
B: glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)78,0992
Polymers78,0992
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-7 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.870, 75.475, 193.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 27 - 346 / Label seq-ID: 27 - 346

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein glutathione S-transferase / / Glutathione transferase


Mass: 39049.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gordonia bronchialis (bacteria) / Strain: ATCC 25592 / DSM 43247 / JCM 3198 / NCTC 10667 / Gene: Gbro_1886 / Production host: Escherichia coli (E. coli) / References: UniProt: D0L9F3, glutathione transferase

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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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate/acetic acid, pH 4.5, 0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 8, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.83→193.71 Å / Num. all: 19214 / Num. obs: 19193 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 12.3
Reflection shellResolution: 2.83→2.99 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2750 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0049refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M1G

3m1g


Resolution: 2.83→96.86 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.882 / SU B: 17.461 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24764 981 5.1 %RANDOM
Rwork0.19993 ---
obs0.20234 18147 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.256 Å2
Baniso -1Baniso -2Baniso -3
1-7.64 Å2-0 Å2-0 Å2
2---3.4 Å20 Å2
3----4.24 Å2
Refinement stepCycle: LAST / Resolution: 2.83→96.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5139 0 0 0 5139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195290
X-RAY DIFFRACTIONr_bond_other_d0.0040.024873
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9537234
X-RAY DIFFRACTIONr_angle_other_deg0.985311177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8085652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25522.789251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8315772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4951546
X-RAY DIFFRACTIONr_chiral_restr0.0820.2782
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216063
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021271
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_it1.6722.8012614
X-RAY DIFFRACTIONr_mcbond_other1.6722.82613
X-RAY DIFFRACTIONr_mcangle_it2.8784.1963264
X-RAY DIFFRACTIONr_mcangle_other2.8774.1973265
X-RAY DIFFRACTIONr_scbond_it1.9722.9552676
X-RAY DIFFRACTIONr_scbond_other1.972.9542676
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4064.3633970
X-RAY DIFFRACTIONr_long_range_B_refined5.09422.2125900
X-RAY DIFFRACTIONr_long_range_B_other5.09422.2175901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 18932 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.83→2.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 58 -
Rwork0.304 1346 -
obs--99.93 %

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