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- PDB-4gf0: Crystal structure of glutahtione transferase homolog from sulfito... -

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Basic information

Entry
Database: PDB / ID: 4gf0
TitleCrystal structure of glutahtione transferase homolog from sulfitobacter, TARGET EFI-501084, with bound glutathione
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / GST / 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 transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-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 transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / 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, putative
Similarity search - Component
Biological speciesSulfitobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of glutahtione transferase homolog from sulfitobacter, TARGET EFI-501084, with bound glutathione
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionAug 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5445
Polymers46,8942
Non-polymers6503
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-39 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.844, 95.844, 94.911
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-446-

HOH

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Components

#1: Protein Glutathione S-transferase


Mass: 23446.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfitobacter (bacteria) / Strain: NAS-14.1 / Gene: NAS141_10626 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3STM0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 0.2 M Lithium Sulfate, 0.1 mM Bis-Tris pH 6.5, 25% PEG3350, 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: Jul 20, 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: 1.75→31.948 Å / Num. all: 45143 / Num. obs: 45143 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.8413.60.79918839865090.799100
1.84-1.9613.70.4931.58377561350.493100
1.96-2.0913.80.3052.57997157830.305100
2.09-2.26140.2093.57575954220.209100
2.26-2.4714.40.1464.97157749860.146100
2.47-2.7714.50.1255.46576445470.125100
2.77-3.214.30.1195.45795340510.119100
3.2-3.9114.10.0966.54863634390.096100
3.91-5.5314.10.05311.23840427250.053100
5.53-31.94812.50.0416.51930015460.0496.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GDR

2gdr


Resolution: 1.75→31.913 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8891 / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / Phase error: 17.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1934 2274 5.05 %RANDOM
Rwork0.1647 ---
all0.1661 45066 --
obs0.1661 45066 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.41 Å2 / Biso mean: 23.0184 Å2 / Biso min: 6.98 Å2
Refinement stepCycle: LAST / Resolution: 1.75→31.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 41 267 3299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063127
X-RAY DIFFRACTIONf_angle_d1.0894269
X-RAY DIFFRACTIONf_chiral_restr0.071495
X-RAY DIFFRACTIONf_plane_restr0.005551
X-RAY DIFFRACTIONf_dihedral_angle_d13.2921150
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.7880.25321420.226226412783100
1.788-1.82960.23281460.19926142760100
1.8296-1.87540.24491670.176726182785100
1.8754-1.92610.25061190.180726522771100
1.9261-1.98280.17451390.167926472786100
1.9828-2.04670.18951290.153826602789100
2.0467-2.11990.18991240.149126602784100
2.1199-2.20470.18651300.15926472777100
2.2047-2.30510.19771580.154926482806100
2.3051-2.42650.17181430.14926592802100
2.4265-2.57850.191480.155626712819100
2.5785-2.77750.17291350.164126762811100
2.7775-3.05680.2071390.170227132852100
3.0568-3.49870.18811610.165626892850100
3.4987-4.40610.16591550.149127462901100
4.4061-31.9130.21151390.17912851299098
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)
11.4882-0.39410.79721.5133-0.98955.6936-0.16790.29320.0083-0.06960.1967-0.14220.06530.274-0.02970.1303-0.00490.01190.1673-0.00310.157643.919321.20388.7705
21.27640.4210.94321.01140.4311.7678-0.0430.1827-0.13760.03420.0840.07680.27080.2128-0.01540.13570.01210.02110.0958-0.00180.132637.89816.92568.2635
31.051-0.03460.24570.99120.14241.2467-0.01930.04650.1150.08690.0329-0.1673-0.09090.6719-0.02090.1418-0.0138-0.03020.25870.00610.15446.090327.930815.3256
41.29090.0436-0.26330.7198-0.16970.7441-0.05480.0835-0.10560.08220.04660.17080.0789-0.0954-0.00870.1275-0.00910.01970.05960.00770.137224.26922.901711.6095
52.32330.74841.07191.85260.9022.5289-0.1454-0.1996-0.12670.12860.182-0.11390.04630.3824-0.06730.26360.09220.02380.24240.01260.127138.058424.042832.1968
61.81360.48570.62390.72970.30410.9784-0.254-0.4885-0.19010.45830.14260.10860.34570.1422-0.2870.44470.15410.08850.23410.09790.10331.887617.955136.472
70.4417-0.8914-0.40662.01360.12043.01960.06860.0377-0.33470.00070.05670.71140.3972-0.41040.03620.1828-0.08720.10790.04810.03360.382219.315411.748115.3086
80.70340.1929-0.17020.372-0.52450.9016-0.2884-0.2271-0.25580.27170.21820.02740.4020.15780.13530.3350.06970.08160.09830.06050.169731.176111.921424.3659
90.71340.6014-0.42571.631-0.6161.67150.0367-0.035-0.2490.17710.13280.16980.1218-0.04940.19510.29230.02260.09190.07310.05910.27825.38845.634420.2356
104.41311.8450.93511.45660.27412.8586-0.13010.0006-0.15150.2080.0588-0.32960.18990.4115-0.05850.23350.01830.03290.0601-0.00150.298137.9448.168611.0815
111.0273-0.0636-0.34770.9843-0.11311.4715-0.0927-0.0901-0.09310.25560.13130.46550.0246-0.1133-0.03360.17650.00850.10830.08630.03990.256913.733734.241219.8106
120.5315-0.37360.26170.5559-0.40432.2547-0.1502-0.22770.08480.2550.1181-0.0567-0.14040.1790.00290.23360.031-0.01370.169-0.01960.132633.607233.920630.1227
130.7483-0.26510.15111.0713-0.10481.1001-0.0558-0.02670.23920.51170.0557-0.0418-0.4090.2083-0.02990.3273-0.01880.01930.0431-0.02520.181426.607446.449521.4645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 11 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 31 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 66 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 103 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 121 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 122 through 146 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 147 through 159 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 160 through 182 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 183 through 193 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 194 through 207 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 87 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 88 through 146 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 147 through 207 )B0

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