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- PDB-4pua: Crystal Structure Of glutathione transferase YghU from Streptococ... -

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Basic information

Entry
Database: PDB / ID: 4pua
TitleCrystal Structure Of glutathione transferase YghU from Streptococcus pneumoniae ATCC 700669, complexed with glutathione, Target EFI-507284
Componentsglutathione S-transferase
KeywordsTRANSFERASE / structural genomics / Enzyme Function Initiative / glutathione
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
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.708 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. / Stead, M. / 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 glutathione transferase YghU from Streptococcus pneumoniae ATCC 700669, complexed with glutathione, Target EFI-507284
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. / Stead, M. / Hillerich, B. / ...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. / Stead, M. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C.
History
DepositionMar 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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_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

Downloads & links

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Assembly

Deposited unit
A: glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2503
Polymers29,6351
Non-polymers6152
Water2,090116
1
A: glutathione S-transferase
hetero molecules

A: glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5006
Polymers59,2712
Non-polymers1,2294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area9840 Å2
ΔGint-67 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.033, 59.887, 170.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein glutathione S-transferase / YghU


Mass: 29635.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC 700669 / Spain 23F-1 / Gene: SPN23F15170 / Production host: Escherichia coli (E. coli) / References: UniProt: B8ZLL4, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M sodium tartrate dibasic, 20% w/v PEG3350, pH 7.0, 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 7, 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: 1.708→85.063 Å / Num. all: 30558 / Num. obs: 30529 / % possible obs: 98.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.5
Reflection shellResolution: 1.708→1.8 Å / Redundancy: 6 % / Rmerge(I) obs: 1.363 / Mean I/σ(I) obs: 2 / Num. unique all: 4317 / % possible all: 97.5

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.8.0049refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MZW

4mzw


Resolution: 1.708→85.06 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.244 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23678 1545 5.1 %RANDOM
Rwork0.18694 ---
obs0.1894 28946 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.741 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0 Å20 Å2
2---2.07 Å2-0 Å2
3---2.43 Å2
Refinement stepCycle: LAST / Resolution: 1.708→85.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 40 116 2234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022171
X-RAY DIFFRACTIONr_bond_other_d0.0010.022033
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9722946
X-RAY DIFFRACTIONr_angle_other_deg0.9134669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2045260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18524.712104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83915343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.605159
X-RAY DIFFRACTIONr_chiral_restr0.1290.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02527
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_it2.1122.3281043
X-RAY DIFFRACTIONr_mcbond_other2.1072.3271042
X-RAY DIFFRACTIONr_mcangle_it3.0933.4871302
X-RAY DIFFRACTIONr_mcangle_other3.0933.4891303
X-RAY DIFFRACTIONr_scbond_it2.7932.5311128
X-RAY DIFFRACTIONr_scbond_other2.7922.5311127
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2953.6971643
X-RAY DIFFRACTIONr_long_range_B_refined5.51418.9462527
X-RAY DIFFRACTIONr_long_range_B_other5.51318.9452528
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.708→1.753 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 112 -
Rwork0.334 2052 -
obs--96.65 %

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