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- PDB-4l8e: Crystal structure of a glutathione transferase family member from... -

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Basic information

Entry
Database: PDB / ID: 4l8e
TitleCrystal structure of a glutathione transferase family member from xenorhabdus nematophila, target efi-507418, with two gsh per subunit
ComponentsGlutathione S-transferase enzyme with thioredoxin-like domain
KeywordsTRANSFERASE / glutathione S-transferase fold / 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, 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 / Putative glutathione S-transferase enzyme with thioredoxin-like domain
Similarity search - Component
Biological speciesXenorhabdus nematophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal structure of a glutathione transferase family member from xenorhabdus nematophila, target efi-507418, with two gsh per subunit
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionJun 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 enzyme with thioredoxin-like domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0736
Polymers26,9201
Non-polymers1,1535
Water3,585199
1
A: Glutathione S-transferase enzyme with thioredoxin-like domain
hetero molecules

A: Glutathione S-transferase enzyme with thioredoxin-like domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,14612
Polymers53,8412
Non-polymers2,30510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Buried area3680 Å2
ΔGint-20 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.331, 65.331, 213.919
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-304-

CL

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Components

#1: Protein Glutathione S-transferase enzyme with thioredoxin-like domain


Mass: 26920.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus nematophila (bacteria) / Strain: ATCC 19061 / Gene: yfcG, XNC1_3157 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D3VKV1
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 7
Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM GSH); Reservoir (0.1 M Sodium Acetate, 0.1 M MES pH 6.5, 30 %(w/v) PEG 400); Cryoprotection (reservoir), sitting drop vapor diffusion, 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: Jun 14, 2013 / 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: 1.7→213.919 Å / Num. all: 29857 / Num. obs: 29857 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.4 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 18.2
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.7921.90.89242842181.00396.7
1.79-1.921.91.18760640030.69197.1
1.9-2.0321.81.98309938110.39997.4
2.03-2.1921.73.17727635540.2497.7
2.19-2.421.74.57162733050.16397.9
2.4-2.6921.55.56484230120.12898.3
2.69-3.121.36.75761927090.09898.6
3.1-3.820.98.44869923270.07298.8
3.8-5.3820.411.13782718560.05598.7
5.38-28.04518.113.61921110620.04694.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GX0

3gx0


Resolution: 1.7→28.045 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8908 / SU ML: 0.12 / σ(F): 1.33 / σ(I): 0 / Phase error: 16.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1759 1501 5.07 %RANDOM
Rwork0.1507 ---
all0.152 29592 --
obs0.152 29592 96.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.46 Å2 / Biso mean: 26.8567 Å2 / Biso min: 9.86 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 67 199 1916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111780
X-RAY DIFFRACTIONf_angle_d1.3812423
X-RAY DIFFRACTIONf_chiral_restr0.085251
X-RAY DIFFRACTIONf_plane_restr0.008316
X-RAY DIFFRACTIONf_dihedral_angle_d14.304657
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 (%)
1.7-1.75490.23351170.20532453257094
1.7549-1.81760.20111210.18812485260695
1.8176-1.89030.19751510.16842418256995
1.8903-1.97640.17991410.15362501264296
1.9764-2.08050.17661480.14052478262696
2.0805-2.21080.17921100.14062554266496
2.2108-2.38140.17331520.13022536268897
2.3814-2.62090.14581470.13532578272597
2.6209-2.99980.17211500.14842580273097
2.9998-3.7780.16591300.14872676280698
3.778-28.04870.18571340.15682832296696
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)
12.6336-0.8119-0.06992.6169-0.2112.42290.01590.18240.006-0.28950.01680.1706-0.0346-0.1686-0.02280.1753-0.0059-0.02950.15560.00410.1264-37.356618.305237.0183
23.4022-3.67480.40638.0378-0.79940.75740.01560.29390.0669-0.63610.0568-0.03720.0994-0.0232-0.07680.2742-0.00110.00030.17050.02380.1222-31.582215.475231.58
33.811-0.71320.77556.8386-0.48811.8352-0.11490.2489-0.0838-0.31930.2187-0.42560.0960.1637-0.10050.1732-0.02070.03140.1827-0.0220.1298-23.390413.608537.9126
43.00871.2326-1.08466.8151-1.8563.96060.11710.08690.5841-0.10020.1429-0.1264-0.7420.5788-0.11750.2612-0.11710.03870.20630.00450.217-24.870527.494539.8222
52.1412-0.1357-0.66492.1605-0.85543.31610.0144-0.05760.26910.11820.09390.1202-0.399-0.2139-0.1080.14630.0175-0.01920.11320.00350.1425-38.824624.546351.3313
61.8242-2.82130.02517.15531.37762.15610.00280.2255-0.32840.1159-0.10030.16910.5481-0.13380.08860.2656-0.04260.01580.1683-0.01110.1893-37.4213-3.275848.1462
74.9629-4.1651-0.10016.42310.05471.9434-0.0453-0.093-0.3810.06170.12470.33350.4913-0.1486-0.08650.2142-0.0545-0.01410.15250.02830.1585-44.19742.009956.3512
84.73312.2083-4.45544.1159-1.14984.5507-0.1259-0.2102-0.08290.32020.01440.2636-0.248-0.40490.13030.15080.0463-0.00520.25870.04420.2434-51.08121.387152.753
93.93162.5199-0.3654.6164-0.7452.3165-0.07930.1206-0.3049-0.4180.19960.4730.4764-0.3541-0.07210.1861-0.0568-0.05680.16450.01560.2068-47.58027.156746.7228
101.52671.5676-1.38227.4483-4.24755.09870.06070.3782-0.2648-0.27950.23050.54320.2992-0.861-0.17130.1094-0.0484-0.05690.31960.0710.2667-54.807613.429945.5913
113.3406-5.1012-1.99878.4591.37665.76560.310.6617-0.1456-0.689-0.24050.45250.1616-0.7332-0.11270.2091-0.012-0.05390.27480.02390.1736-48.099117.452334.7152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 7:27 )A7 - 27
2X-RAY DIFFRACTION2( CHAIN A AND RESID 28:41 )A28 - 41
3X-RAY DIFFRACTION3( CHAIN A AND RESID 42:62 )A42 - 62
4X-RAY DIFFRACTION4( CHAIN A AND RESID 63:76 )A63 - 76
5X-RAY DIFFRACTION5( CHAIN A AND RESID 77:111 )A77 - 111
6X-RAY DIFFRACTION6( CHAIN A AND RESID 112:131 )A112 - 131
7X-RAY DIFFRACTION7( CHAIN A AND RESID 132:153 )A132 - 153
8X-RAY DIFFRACTION8( CHAIN A AND RESID 154:165 )A154 - 165
9X-RAY DIFFRACTION9( CHAIN A AND RESID 166:188 )A166 - 188
10X-RAY DIFFRACTION10( CHAIN A AND RESID 189:200 )A189 - 200
11X-RAY DIFFRACTION11( CHAIN A AND RESID 201:209 )A201 - 209

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