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- PDB-4ibp: Crystal structure of a glutathione transferase family member from... -

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Basic information

Entry
Database: PDB / ID: 4ibp
TitleCrystal structure of a glutathione transferase family member from Pseudomonas fluorescens Pf-5, target EFI-900011, with bound glutathione
ComponentsGlutathione S-transferase-like protein YibF
KeywordsTRANSFERASE / GST / 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 Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like 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 Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-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 / Glutathione S-transferase-like protein YibF
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVetting, M.W. / Sauder, J.M. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Burley, S.K. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a glutathione transferase family member from Pseudomonas fluorescens Pf-5, target IFI-900011, with bound glutathione
Authors: Vetting, M.W. / Sauder, J.M. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Burley, S.K. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionDec 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Structure summary
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase-like protein YibF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8173
Polymers24,4131
Non-polymers4032
Water1,892105
1
A: Glutathione S-transferase-like protein YibF
hetero molecules

A: Glutathione S-transferase-like protein YibF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6336
Polymers48,8262
Non-polymers8074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y,-z1
Buried area6230 Å2
ΔGint-48 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.531, 81.915, 111.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-476-

HOH

21A-480-

HOH

31A-504-

HOH

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Components

#1: Protein Glutathione S-transferase-like protein YibF


Mass: 24413.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf-5 / Gene: yibF, PFL_5710 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4K4R5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl); Reservoir (0.1 M Bis-Tris Propane:HCl pH 7.0, 1.8 M Magnesium Sulfate); Cryoprotection (20 mM Bis-Tris Propane:HCl pH 7.0, 2.2 M Magnesium Sulfate ...Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl); Reservoir (0.1 M Bis-Tris Propane:HCl pH 7.0, 1.8 M Magnesium Sulfate); Cryoprotection (20 mM Bis-Tris Propane:HCl pH 7.0, 2.2 M Magnesium Sulfate + 2 mM reduce glutathione), 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 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 8, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→38.66 Å / Num. all: 30206 / Num. obs: 30206 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Biso Wilson estimate: 40.46 Å2 / Rmerge(I) obs: 0.094
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4410 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TOU

3tou


Resolution: 1.8→38.659 Å / Occupancy max: 1 / Occupancy min: 0.9 / FOM work R set: 0.7046 / SU ML: 0.22 / σ(F): 0 / σ(I): 0 / Phase error: 34.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 1523 5.05 %RANDOM
Rwork0.2198 ---
all0.2214 30135 --
obs0.2214 30135 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.44 Å2 / Biso mean: 50.0895 Å2 / Biso min: 30.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 25 105 1758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071691
X-RAY DIFFRACTIONf_angle_d1.1092306
X-RAY DIFFRACTIONf_chiral_restr0.072253
X-RAY DIFFRACTIONf_plane_restr0.004303
X-RAY DIFFRACTIONf_dihedral_angle_d14.482638
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.85810.41581440.43325872731100
1.8581-1.92450.45471390.38892531267099
1.9245-2.00160.38571200.346626402760100
2.0016-2.09260.38511410.29972559270099
2.0926-2.2030.28371280.281426132741100
2.203-2.3410.31211410.253926082749100
2.341-2.52170.31340.243826202754100
2.5217-2.77540.27251470.243326172764100
2.7754-3.17680.29231290.234326382767100
3.1768-4.00180.22791550.186726482803100
4.0018-38.6680.18361450.17792551269692

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