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- PDB-5hfk: CRYSTAL STRUCTURE OF A GLUTATHIONE S-TRANSFERASE PROTEIN FROM ESC... -

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Entry
Database: PDB / ID: 5hfk
TitleCRYSTAL STRUCTURE OF A GLUTATHIONE S-TRANSFERASE PROTEIN FROM ESCHERICHIA COLI OCh 157:H7 STR. SAKAI (ECs3186, TARGET EFI-507414) WITH BOUND GLUTATHIONE
ComponentsDisulfide-bond oxidoreductase YfcG
KeywordsTRANSFERASE / GLUTATHIONE S-TRANSFERASE FAMILY / ENZYME FUNCTION INITIATIVE (EFI) / STRUCTURAL GENOMICS / GLUTATHIONE LIGANDS / New York Structural Genomics Research Consortium / NYSGRC / OXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / disulfide oxidoreductase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / response to oxidative stress / protein homodimerization 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / 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 ...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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / 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 / Disulfide-bond oxidoreductase YfcG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 Å
AuthorsHimmel, D.M. / Toro, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. ...Himmel, D.M. / Toro, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) / New York Structural Genomics Research Consortium (NYSGRC)
Citation
Journal: TO BE PUBLISHED
Title: CRYSTAL STRUCTURE OF A GLUTATHIONE S-TRANSFERASE PROTEIN FROM ESCHERICHIA COLI OCh 157:H7 STR. SAKAI (ECs3186, TARGET EFI-507414) WITH BOUND GLUTATHIONE
Authors: Himmel, D.M. / Toro, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Evans, B. / ...Authors: Himmel, D.M. / Toro, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
#1: Journal: Biochemistry / Year: 2011
Title: Structure and function of YghU, a nu-class glutathione transferase related to YfcG from Escherichia coli.
Authors: Stourman, N.V. / Branch, M.C. / Schaab, M.R. / Harp, J.M. / Ladner, J.E. / Armstrong, R.N.
#2: Journal: Biochemistry / Year: 2009
Title: Analysis of the structure and function of YfcG from Escherichia coli reveals an efficient and unique disulfide bond reductase.
Authors: Wadington, M.C. / Ladner, J.E. / Stourman, N.V. / Harp, J.M. / Armstrong, R.N.
History
DepositionJan 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disulfide-bond oxidoreductase YfcG
B: Disulfide-bond oxidoreductase YfcG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2066
Polymers53,9772
Non-polymers1,2294
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-38 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.267, 83.267, 171.153
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Disulfide-bond oxidoreductase YfcG / GSH-dependent disulfide-bond oxidoreductase YfcG / GST N1-1 / GST-like protein YfcG / Organic hydroperoxidase


Mass: 26988.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Several N-terminal and carboxy-terminal residues for each chain were disordered in the structure, according to the electron density.
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: yfcG, b2302, JW2299 / Plasmid: pSGC-His / Details (production host): Alias: pNIC28-Bsa4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P77526, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence matches to GenBank Accession #NP_311213.1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein (18.49 mg/ml, 20 mM HEPES pH 7.5, 0.150 M Sodium Chloride, 5% v/v Glycerol, 4.5 mM DTT, 5 mM reduced Glutathione) were combined with an equal volume of Reservoir (100 mM Bis-tris pH ...Details: Protein (18.49 mg/ml, 20 mM HEPES pH 7.5, 0.150 M Sodium Chloride, 5% v/v Glycerol, 4.5 mM DTT, 5 mM reduced Glutathione) were combined with an equal volume of Reservoir (100 mM Bis-tris pH 6.5, 100 mM Magnesium Chloride, 2.8 M Sodium Chloride); Cryoprotection (Equal volumes of Reservoir + 50% v/v Glycerol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 13, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Num. obs: 86041 / % possible obs: 98.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 16.72 Å2 / Rmerge(I) obs: 0.093 / Χ2: 1.005 / Net I/av σ(I): 16.983 / Net I/σ(I): 11.6 / Num. measured all: 614788
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.55-1.613.30.4212.65379610.95692.5
1.61-1.674.10.41584100.99397.5
1.67-1.754.50.38984450.99597.8
1.75-1.845.10.35585141.00798.1
1.84-1.955.90.30685291.0198.3
1.95-2.17.20.23386431.00899.2
2.1-2.318.40.1786831.00399.3
2.31-2.659.50.1487531.00899.4
2.65-3.3310.60.11888671.00599.6
3.33-2011.90.06692361.01599.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Coot0.8model building
HKL-20002.0.0data reduction
SCALEPACK1.99.2data scaling
PHASES2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GX0

3gx0


Resolution: 1.551→19.655 Å / Rfactor Rfree error: 0.003 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 23.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2125 4282 4.98 %
Rwork0.1855 81703 -
obs0.1868 85985 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.32 Å2 / Biso mean: 24.4518 Å2 / Biso min: 10.47 Å2
Refinement stepCycle: final / Resolution: 1.551→19.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 80 361 3765
Biso mean--28.04 34.52 -
Num. residues----412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013520
X-RAY DIFFRACTIONf_angle_d1.1884790
X-RAY DIFFRACTIONf_chiral_restr0.07501
X-RAY DIFFRACTIONf_plane_restr0.008625
X-RAY DIFFRACTIONf_dihedral_angle_d14.0051282
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 (%)
1.5508-1.56840.39571260.38782196232281
1.5684-1.58690.37081530.38622568272195
1.5869-1.60620.39611410.37262635277696
1.6062-1.62650.39071430.36312646278997
1.6265-1.64790.39511400.36812660280097
1.6479-1.67050.35091310.34532704283598
1.6705-1.69440.35191340.33592695282997
1.6944-1.71960.34761480.32772650279898
1.7196-1.74650.35361340.3152703283798
1.7465-1.77510.33221410.29942710285198
1.7751-1.80570.29891190.27612717283698
1.8057-1.83850.29221500.26672682283298
1.8385-1.87380.27261190.24732720283999
1.8738-1.91210.28531220.23662709283198
1.9121-1.95360.21371390.22352726286599
1.9536-1.9990.24851790.19942719289899
1.999-2.04890.19811360.18262735287199
2.0489-2.10430.23761390.17992752289199
2.1043-2.16610.18741460.160727502896100
2.1661-2.23590.20351640.14922730289499
2.2359-2.31570.17841590.15232761292099
2.3157-2.40830.17281400.146627672907100
2.4083-2.51770.15151440.150927842928100
2.5177-2.65010.17281470.15012752289999
2.6501-2.81570.17141530.149227932946100
2.8157-3.03240.16791530.159428042957100
3.0324-3.33620.1681380.155128492987100
3.3362-3.81590.17461360.137428562992100
3.8159-4.79610.15371530.129528873040100
4.7961-19.65690.19761550.15530433198100
Refinement TLS params.

Details: Portion of GSH ligand / 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)
12.01751.97131.97862.01942.00962.00260.0135-0.2126-1.3647-2.33730.22451.03361.2185-1.4737-0.12970.5125-0.189-0.1590.57850.19220.457553.620738.439967.7933
27.3135-4.70646.08564.8643-3.63415.10771.3166-1.0651-0.35586.0096-1.4329-2.18910.48110.010.00920.5512-0.0017-0.00740.4450.14070.347455.892841.801870.984
35.55595.44342.0035.33271.9731.99090.84271.20340.229-0.1183-0.7547-0.15120.4513-1.0352-0.07130.22920.0146-0.03390.41990.0160.288459.266238.99672.5812
44.34553.73893.7453.24033.3343.87730.3605-0.05770.57950.2106-0.1437-0.2032-0.4817-0.3137-0.16210.19040.01470.02040.19760.05660.21963.265640.752369.8783
56.91548.23087.43049.79938.84577.9860.6965-0.63010.267-0.7332-0.3280.5542-0.3171-1.9392-0.61470.24290.02370.0110.30450.10740.174458.751143.175268.623
66.14786.33871.93176.5611.71833.21390.5319-2.42740.34560.3227-2.32.55320.8117-3.05311.75710.1906-0.0334-0.06090.3936-0.07480.366556.90141.313664.6031
72.00891.95812.02642.02271.95752.0479-1.1969-0.24361.52890.4625-0.09471.2693-0.6219-0.72781.36830.2752-0.011-0.02430.64380.24760.663759.699623.455880.6936
81.99992-2.08072.001-0.82691.22942.61064.24681.3614-2.1946-3.0748-2.30210.90262.20430.42490.45730.2641-0.03720.72570.2490.177363.595722.692677.6172
91.76632.31121.25186.22234.95544.32990.6305-0.7304-0.15520.9234-1.28120.34470.1072-0.47060.63760.3176-0.0360.08570.32380.07420.302464.053227.099975.9532
1022.00142.00231.99881.99915.25870.38370.42790.0585-0.2283-0.1949-0.51750.0076-0.0919-0.210.1692-0.02820.01580.23140.04560.260468.126428.570778.6746
115.82714.7334-3.51235.7266-0.87664.18890.09740.7957-0.86062.0552-0.2280.08042.144-0.58570.14840.33450.0113-0.03930.23090.02860.217566.599623.715479.9559
125.7894-1.03714.62260.2751-1.21185.3427-1.21970.7022-3.86740.599-0.08331.31381.0683-1.57381.27270.3744-0.10230.10420.26310.01580.275963.925823.74583.9661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESSEQ 302) AND (NAME O2 OR NAME N3 OR NAME CA3 OR NAME C3 OR NAME O31 OR NAME O32)B0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESSEQ 301) AND (NAME CD1 OR NAME N2 OR NAME CA2 OR NAME CB2 OR NAME SG2 OR NAME C2)A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESSEQ 301) AND (NAME O2 OR NAME N3 OR NAME CA3 OR NAME C3 OR NAME O31 OR NAME O32)A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESSEQ 302) AND (NAME N1 OR NAME CA1 OR NAME C1 OR NAME O11 OR NAME O12 OR NAME CB1 OR NAME CG1 OR NAME O1)A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESSEQ 302) AND (NAME CD1 OR NAME N2 OR NAME CA2 OR NAME CB2 OR NAME SG2 OR NAME C2)A0
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESSEQ 302) AND (NAME O2 OR NAME N3 OR NAME CA3 OR NAME C3 OR NAME O31 OR NAME O32)A0
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESSEQ 301) AND (NAME N1 OR NAME CA1 OR NAME C1 OR NAME O11 OR NAME O12 OR NAME CB1 OR NAME CG1 OR NAME O1)B0
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESSEQ 301) AND (NAME CD1 OR NAME N2 OR NAME CA2 OR NAME CB2 OR NAME SG2 OR NAME C2)B0
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESSEQ 301) AND (NAME O2 OR NAME N3 OR NAME CA3 OR NAME C3 OR NAME O31 OR NAME O32)B0
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESSEQ 302) AND (NAME N1 OR NAME CA1 OR NAME C1 OR NAME O11 OR NAME O12 OR NAME CB1 OR NAME CG1 OR NAME O1)B0
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESSEQ 302) AND (NAME CD1 OR NAME N2 OR NAME CA2 OR NAME CB2 OR NAME SG2 OR NAME C2)B0
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESSEQ 302) AND (NAME O2 OR NAME N3 OR NAME CA3 OR NAME C3 OR NAME O31 OR NAME O32)B0

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