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Basic information

Entry
Database: PDB / ID: 4id0
TitleCrystal structure of a glutathione transferase family member from Pseudomonas fluorescens Pf-5, target EFI-900011, with bound glutathione sulfinic acid (gso2h) and acetate
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
ACETATE ION / L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE / Glutathione S-transferase-like protein YibF
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 EFI-900011, with bound glutathione sulfinic acid (gso2h) and acetate
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 11, 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
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,4948
Polymers48,8262
Non-polymers6686
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-23 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.542, 69.741, 80.182
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24413.176 Da / Num. of mol.: 2
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GSF / L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE / GLUTATHIONE SULFINATE


Mass: 339.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O8S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl + 5 mM Reduced glutathione); Reservoir (200 mM AmAcetate, 100 mM Na3Citrate pH 5.6, 25% Peg4000, 15% glycerol); Cryoprotection (90% reservoir, 10% ...Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl + 5 mM Reduced glutathione); Reservoir (200 mM AmAcetate, 100 mM Na3Citrate pH 5.6, 25% Peg4000, 15% glycerol); Cryoprotection (90% reservoir, 10% glycerol), 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: 1.1→22.3 Å / Num. all: 142316 / Num. obs: 1904924 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 7.88 Å2 / Rmerge(I) obs: 0.096
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 8 % / Rmerge(I) obs: 0.0523 / Mean I/σ(I) obs: 3.6 / Num. unique all: 12821 / % possible all: 57

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Processing

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

3tou


Resolution: 1.1→22.015 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.9094 / SU ML: 0.08 / σ(F): 0 / σ(I): 0 / Phase error: 15.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1718 7132 5.01 %RANDOM
Rwork0.1583 ---
all0.159 142239 --
obs0.159 142239 91.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 42.58 Å2 / Biso mean: 11.3827 Å2 / Biso min: 3.36 Å2
Refinement stepCycle: LAST / Resolution: 1.1→22.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 44 614 3900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153507
X-RAY DIFFRACTIONf_angle_d1.6564798
X-RAY DIFFRACTIONf_chiral_restr0.099520
X-RAY DIFFRACTIONf_plane_restr0.01644
X-RAY DIFFRACTIONf_dihedral_angle_d13.6481307
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.11250.23541150.21772201231645
1.1125-1.12560.19751280.20182572270052
1.1256-1.13930.18451400.18492916305660
1.1393-1.15370.16891450.18453189333465
1.1537-1.16890.20891850.18443538372372
1.1689-1.18490.19682130.18433821403479
1.1849-1.20190.20152130.19374309452288
1.2019-1.21980.19992560.18314646490295
1.2198-1.23880.18912700.17284741501198
1.2388-1.25920.19442600.17184764502498
1.2592-1.28090.17572760.16854794507098
1.2809-1.30420.16122520.15774845509798
1.3042-1.32920.19212520.15524793504598
1.3292-1.35640.17022450.15084862510799
1.3564-1.38590.15992570.15094822507999
1.3859-1.41810.17712470.15264875512299
1.4181-1.45350.16453010.1474828512999
1.4535-1.49280.14852710.14144840511199
1.4928-1.53680.14942570.13624867512499
1.5368-1.58630.15312590.13344935519499
1.5863-1.6430.14232270.13774918514599
1.643-1.70880.17582750.140949505225100
1.7088-1.78650.15322690.14749145183100
1.7865-1.88070.16392420.149549585200100
1.8807-1.99840.15272550.154549645219100
1.9984-2.15260.1642810.149749415222100
2.1526-2.3690.16972780.158549845262100
2.369-2.71130.18682550.170250305285100
2.7113-3.41380.16982540.16550855339100
3.4138-22.01960.1842540.16275205545999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5390.06880.0830.93460.43820.798-0.0095-0.05250.05580.0592-0.01610.1536-0.0151-0.0890.02490.0616-0.00140.00530.06530.00730.0678-16.8239-0.5978-6.5052
21.0223-0.2091-0.00971.65690.3991.4901-0.0086-0.1038-0.13290.1440.00030.13010.0889-0.1135-0.00070.0396-0.01180.00370.05170.01460.0475-13.6493-8.2631-1.4698
33.2540.5311-0.03580.22290.44491.54950.0624-0.079-0.69620.2717-0.0321-0.16450.4125-0.0106-0.09170.1381-0.00880.01060.06420.01970.1809-4.736-19.3502-9.139
40.6251-0.73080.19583.31-0.08790.51260.0430.0341-0.11150.0153-0.02740.27540.0325-0.0206-0.01790.0447-0.008-0.00430.05390.00220.06010.77941.1472-8.4241
50.42420.10120.09730.86140.43470.3914-0.01110.08320.0167-0.07340.0592-0.0815-0.0520.0397-0.04490.054-0.00760.00890.05210.00730.04073.22286.4059-14.9834
61.93820.2481-0.48920.3890.09820.84840.0114-0.07630.0415-0.05660.02880.0013-0.04610.0405-0.04630.0695-0.01010.00210.0627-0.00860.0518-5.1649-3.0576-23.8242
70.74550.1264-0.0320.8475-0.51961.2681-0.0154-0.0406-0.03010.0121-0.005-0.0690.03340.07470.01550.0350.0113-0.00450.048-0.00040.053911.8909-3.80633.6434
80.52-0.32790.09530.2188-0.14780.49070.0076-0.1131-0.1555-0.0473-0.0161-0.07970.0572-0.0186-0.02130.05320.0067-0.00380.06160.01910.0731-2.5502-3.73236.6292
91.56890.9258-1.03722.1721-1.29291.6940.05-0.07020.15380.12750.07580.1637-0.1115-0.081-0.1120.06040.0134-0.00530.068-0.01190.0429-7.09814.13687.6397
100.7977-0.0727-0.14550.96960.09851.23820.0154-0.1551-0.02380.15320.02450.03160.021-0.0495-0.03080.06320.0123-0.00130.10540.0090.0344-1.1551.317118.9943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 52 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 77 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 87 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 117 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 118 through 181 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 182 through 203 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 76 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 77 through 117 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 118 through 147 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 148 through 203 )B0

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