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Basic information

Entry
Database: PDB / ID: 4iji
TitleCrystal structure of a glutathione transferase family member from Psuedomonas fluorescens Pf-5, target EFI-900011, with bound S-(propanoic acid)-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
Chem-99T / ACRYLIC ACID / BENZOIC ACID / Glutathione S-transferase-like protein YibF
Similarity search - Component
Biological speciesPseudomonas protegens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 Psuedomonas fluorescens Pf-5, target EFI-900011, with bound S-(propanoic acid)-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 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.2Feb 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 1.3Sep 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 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 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
C: Glutathione S-transferase-like protein YibF
D: Glutathione S-transferase-like protein YibF
E: Glutathione S-transferase-like protein YibF
F: Glutathione S-transferase-like protein YibF
G: Glutathione S-transferase-like protein YibF
H: Glutathione S-transferase-like protein YibF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,97018
Polymers195,3058
Non-polymers2,66510
Water40,1552229
1
A: Glutathione S-transferase-like protein YibF
F: Glutathione S-transferase-like protein YibF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4005
Polymers48,8262
Non-polymers5743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-8 kcal/mol
Surface area16700 Å2
MethodPISA
2
B: Glutathione S-transferase-like protein YibF
C: Glutathione S-transferase-like protein YibF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5854
Polymers48,8262
Non-polymers7592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-12 kcal/mol
Surface area16330 Å2
MethodPISA
3
D: Glutathione S-transferase-like protein YibF
H: Glutathione S-transferase-like protein YibF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4005
Polymers48,8262
Non-polymers5743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-6 kcal/mol
Surface area16710 Å2
MethodPISA
4
E: Glutathione S-transferase-like protein YibF
G: Glutathione S-transferase-like protein YibF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5854
Polymers48,8262
Non-polymers7592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-12 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.763, 190.002, 83.600
Angle α, β, γ (deg.)90.00, 101.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24413.176 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens (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-99T / L-gamma-glutamyl-S-(2-carboxyethyl)-L-cysteinylglycine / S-(propanoic acid)glutathione


Mass: 379.386 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H21N3O8S
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2229 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl + 5 mM Reduced glutathione); Reservoir (0.02 M Magnesium Chloride 0.1 M HEPES:NaOH pH 7.5 22% (w/v) Polyacrylic Acid 5100); Cryoprotection (20% ...Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl + 5 mM Reduced glutathione); Reservoir (0.02 M Magnesium Chloride 0.1 M HEPES:NaOH pH 7.5 22% (w/v) Polyacrylic Acid 5100); Cryoprotection (20% reservoir, 80% (50% (w/v) Polyacrylic acid); glutathione adduct presumably arising from gluathione attack of free acrylate, benozic acid like molecule of unknown origins, vapor diffusion, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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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: 1.5→95.001 Å / Num. all: 260818 / Num. obs: 260818 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.585.10.5751.4189399372400.57596
1.58-1.685.30.3982187611355410.39897
1.68-1.795.50.2952.6185158336280.29597.6
1.79-1.945.80.1914.1182914315720.19198.4
1.94-2.126.10.1216.4177904291580.12198.8
2.12-2.376.40.098.3169402264630.0999
2.37-2.746.70.0779.4157855234510.07799.4
2.74-3.357.20.05811.8142752198790.05899.8
3.35-4.747.60.04316.1117219154490.043100
4.74-95.0017.50.04814.36364384370.04899.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ID0

4id0


Resolution: 1.5→36.27 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8847 / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1976 13130 5.04 %RANDOM
Rwork0.1694 ---
obs0.1708 260723 98.05 %-
all-260723 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.61 Å2 / Biso mean: 19.3684 Å2 / Biso min: 4.52 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12725 0 178 2229 15132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613331
X-RAY DIFFRACTIONf_angle_d1.0718170
X-RAY DIFFRACTIONf_chiral_restr0.0671999
X-RAY DIFFRACTIONf_plane_restr0.0052391
X-RAY DIFFRACTIONf_dihedral_angle_d14.1324962
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 (%)
1.5-1.5170.28134330.24378033846695
1.517-1.53490.26634340.24138002843696
1.5349-1.55360.29124510.23668086853796
1.5536-1.57330.2674610.22648055851696
1.5733-1.5940.24773890.21388054844396
1.594-1.61580.25714240.21198181860597
1.6158-1.63890.23064370.1978110854797
1.6389-1.66340.2254850.19448144862997
1.6634-1.68940.25194050.19698127853297
1.6894-1.71710.24394590.1978238869798
1.7171-1.74670.22874190.18668152857198
1.7467-1.77840.22644130.18868289870298
1.7784-1.81260.23564200.18578275869598
1.8126-1.84960.20414270.17548222864998
1.8496-1.88980.20644380.17448293873198
1.8898-1.93380.20684390.17338230866998
1.9338-1.98220.21854540.1778272872699
1.9822-2.03570.20664410.17538356879799
2.0357-2.09560.21154150.16838336875199
2.0956-2.16330.19444350.16278266870199
2.1633-2.24060.19934400.16148317875799
2.2406-2.33030.18974280.15698366879499
2.3303-2.43630.17964270.15798353878099
2.4363-2.56470.20344370.16348376881399
2.5647-2.72540.18724440.16438390883499
2.7254-2.93570.1914720.163283318803100
2.9357-3.2310.18984560.161984608916100
3.231-3.69810.15644660.151883698835100
3.6981-4.65770.16164540.138284648918100
4.6577-36.28030.18094270.1698446887399
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)
10.0892-0.0085-0.03220.0107-0.00330.0623-0.0561-0.0850.0349-0.0577-0.0250.0384-0.0771-0.0171-0.02130.0799-0.0132-0.02830.0617-0.01860.076119.923310.717513.4883
20.04030.0281-0.04160.0216-0.02940.044-0.0224-0.0211-0.0005-0.0075-0.05170.027-0.0285-0.0115-0.02920.08580.0066-0.02970.0626-0.03010.047611.3895-2.41339.5284
30.01420.00470.003-0.0003-0.00010.001-0.01490.0062-0.0141-0.0486-0.04690.0475-0.0098-0.0422-0.01910.1212-0.0056-0.01280.1106-0.02720.07081.9458-3.6894-0.9406
40.03490.02760.0120.0285-0.00210.0398-0.0307-0.03470.069-0.0097-0.02040.0805-0.0002-0.0804-0.0177-0.02890.00680.05170.1297-0.08290.06811.98942.370416.8161
50.0434-0.00410.02020.01130.02610.12360.05470.0304-0.0394-0.0028-0.0045-0.020.0721-0.06350.0110.0441-0.0075-0.0180.0647-0.01280.067531.717119.075636.2466
60.0103-0.0020.0057-0.001-0.00340.01770.0353-0.02890.0284-0.0028-0.00480.0140.019-0.01130.01370.0578-0.0078-0.00560.0776-0.00550.047933.531531.67445.7172
70.0019-0.0048-0.00310.0030.00540.00810.0161-0.04790.05040.0591-0.03740.0201-0.0140.00190.00410.1133-0.0023-0.03250.1338-0.01750.084135.181635.713557.4314
80.00560.0023-0.00620.0023-0.00220.00610.0145-0.00060.0360.0164-0.00990.0679-0.0287-0.0843-0.0047-0.15140.03960.05220.1667-0.03630.063720.762831.79846.5189
90.0160.01080.0020.00890.00170.00010.00380.04040.02410.00710.0301-0.0103-0.03160.02860.01110.0467-0.01750.00650.0657-0.01030.087650.385440.366436.1053
100.00050.0004-0.00030.00090.00060.00240.00470.01340.00370.00050.00050.0072-0.0054-0.0013-00.1494-0.0450.01690.12410.0160.140949.382448.051232.2201
11-00-0.0001-00.00010.0002-0.0029-0.0146-0.00120.0103-0.0068-0.0038-0.00490.0026-00.1306-0.02530.01890.1161-0.01190.131743.360142.376248.5661
120.0016-0.00060.00210.00030.00050.0039-0.01090.02370.0210.0018-0.00460.0197-0.0147-0.0066-0.00190.07110.0016-0.01360.0625-0.0010.111139.279941.982233.4039
130.0002-0.00050.00040.0007-0.00050.00020.00180.00640-0.0130.00140.0144-0.01060.004700.0995-0.0048-0.01470.1881-0.01510.070743.589734.350221.3464
140.0013-0.00130.00180.0007-0.00150.01680.03150.0077-0.01350.0161-0.0128-0.0107-0.04420.0217-0.00020.0408-0.0075-0.00050.086-0.01870.060646.504126.317840.6587
150.00850.0117-0.00360.0241-0.00880.00310.05980.0195-0.05640.0348-0.0443-0.01910.01410.01910.00430.06980.0167-0.03220.0781-0.0220.079350.348320.133251.6351
160.01840.00360.01870.00030.00620.0210.00970.0269-0.0201-0.00090.0217-0.03290.00410.07240.0297-0.0643-0.01150.00710.1992-0.08270.113958.395527.070736.3623
170.06930.00390.06240.03090.02330.05940.0008-0.1171-0.02380.07440.0371-0.03170.0625-0.0450.00480.081-0.0058-0.00340.0589-0.0030.076424.711536.13894.1284
180.0049-00.005-0.00010.00410.0194-0.0157-0.01440.0522-0.0478-0.03610.0752-0.0047-0.0462-0.00010.1154-0.01370.0340.1024-0.03140.196110.372549.913-7.9619
190.0252-00.01210.00750.01690.03490.03130.0101-0.0253-0.0501-0.0155-0.01110.0329-0.04550.03090.1398-0.0288-0.00420.0502-0.03770.025620.899835.248-12.6218
200.03070.0167-0.02240.0336-0.01840.0371-0.05170.06580.0366-0.02010.05520.0255-0.0221-0.075-0.01180.10030.00120.00590.07870.01930.049236.6391-5.829239.0603
210.1065-0.00480.00030.03760.00320.0063-0.0314-0.0802-0.05840.0428-0.0157-0.0229-0.0329-0.008-0.00540.06370.0010.00080.03420.0020.043740.912-13.912856.1379
220.00730.00390.00180.0110.00760.01830.04790.0093-0.04370.01230.00150.00050.0510.00260.02920.0739-0.00380.00110.0592-0.01010.075620.8873-15.84356.6096
230.03950.05450.03830.09410.05050.0909-0.0490.0702-0.035-0.10580.0174-0.0713-0.06850.1237-0.0090.055-0.01720.00240.0788-0.0140.027728.215-1.8274-3.0895
240.0172-0.0069-0.00190.0124-0.00140.0056-0.07250.0122-0.0979-0.08090.0271-0.06320.07950.0066-0.0120.1507-0.0080.05290.0658-0.01320.11240.9734-31.69441.6317
250.00450.0051-0.00380.01080.00480.0061-0.01440.0079-0.0332-0.04580.04190.0204-0.0110.01120.00340.146-0.04190.01790.11660.00980.072828.546-21.522840.0213
260.0047-0.00210.00130.0039-0.0020.0009-0.02340.04540.0344-0.01620.02940.0535-0.0246-0.0051-0.00340.1681-0.0130.02910.15960.08650.157517.5068-20.156346.7253
270.00320.0052-0.00070.0062-0.00110.0016-0.01220.0405-0.0075-0.06090.03890.00150.017-0.01540.04950.2464-0.213-0.04910.2403-0.04250.071822.9646-30.349232.6486
280.02110.0010.0020.007-0.01430.03660.0131-0.00860.0545-0.04250.044-0.0538-0.0350.00990.02350.0775-0.02230.03510.0283-0.02430.138631.86359.2979-0.8405
290.0399-0.0041-0.00250.10230.02060.03380.0052-0.02840.03310.22050.00030.03140.0148-0.02250.04150.09710.0070.01260.0798-0.04290.122223.013954.36414.3772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 87 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 116 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 145 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 203 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 89 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 90 through 117 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 118 through 145 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 146 through 203 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 22 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 23 through 32 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 33 through 54 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 55 through 76 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 77 through 87 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 88 through 117 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 118 through 145 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 146 through 204 )C0
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 117 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 118 through 145 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 146 through 203 )D0
20X-RAY DIFFRACTION20chain 'E' and (resid 0 through 87 )E0
21X-RAY DIFFRACTION21chain 'E' and (resid 88 through 203 )E0
22X-RAY DIFFRACTION22chain 'F' and (resid 0 through 76 )F0
23X-RAY DIFFRACTION23chain 'F' and (resid 77 through 204 )F0
24X-RAY DIFFRACTION24chain 'G' and (resid 0 through 88 )G0
25X-RAY DIFFRACTION25chain 'G' and (resid 89 through 116 )G0
26X-RAY DIFFRACTION26chain 'G' and (resid 117 through 146 )G0
27X-RAY DIFFRACTION27chain 'G' and (resid 147 through 203 )G0
28X-RAY DIFFRACTION28chain 'H' and (resid 0 through 74 )H0
29X-RAY DIFFRACTION29chain 'H' and (resid 75 through 207 )H0

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