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Basic information

Entry
Database: PDB / ID: 4mk3
TitleCrystal structure of a glutathione transferase family member from Cupriavidus metallidurans CH34, target EFI-507362, with bound glutathione sulfinic acid (gso2h)
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / GST / glutathione S-transferase fold / Enzyme Function Initiative / EFI / structural genomics
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
Uncharacterized GST-like protein YibF / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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 / 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 ...Uncharacterized GST-like protein YibF / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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 / 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
L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE / Glutathione S-transferase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsToro, R. / Bhosle, R. / Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. ...Toro, R. / Bhosle, R. / Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / 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 Cupriavidus metallidurans CH34, target EFI-507362, with bound glutathione sulfinic acid (gso2h)
Authors: Toro, R. / Bhosle, R. / Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / ...Authors: Toro, R. / Bhosle, R. / Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C.
History
DepositionSep 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4085
Polymers25,6561
Non-polymers7524
Water3,747208
1
A: Glutathione S-transferase
hetero molecules

A: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,81610
Polymers51,3122
Non-polymers1,5048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area6640 Å2
ΔGint-23 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.611, 70.611, 89.553
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 Glutathione S-transferase / / GST


Mass: 25656.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Strain: CH34 / ATCC 43123 / DSM 2839 / Gene: gst-1, Rmet_2957 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1LJ46, glutathione transferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#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 / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: protein (21.88 mg/mL in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, 5 mM GSH), reservoir (0.1 M MES, pH 6.5, 0.1 M magnesium chloride, 30% PEG400), cryoprotection (reservoir + ...Details: protein (21.88 mg/mL in 10 mM HEPES, pH 7.5, 150 mM sodium chloride, 5% glycerol, 5 mM GSH), reservoir (0.1 M MES, pH 6.5, 0.1 M magnesium chloride, 30% PEG400), cryoprotection (reservoir + 20% diethylene glycol), 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: Jun 23, 2013 / Details: mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→100 Å / Num. all: 36929 / Num. obs: 36929 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Χ2: 2.179 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.5314.20.63317911.2011100
1.53-1.5514.30.60318051.1811100
1.55-1.5814.30.49818231.2311100
1.58-1.6214.30.40518111.2661100
1.62-1.6514.40.37118151.2891100
1.65-1.6914.40.33518261.3181100
1.69-1.7314.40.28518171.3691100
1.73-1.7814.50.24918211.3691100
1.78-1.8314.50.22218111.4591100
1.83-1.8914.50.17918301.531100
1.89-1.9614.50.14918361.621100
1.96-2.0414.40.12918391.9931100
2.04-2.1314.30.1218362.6151100
2.13-2.2413.90.11418393.1311100
2.24-2.3813.40.10318483.4921100
2.38-2.5613.10.09418623.9031100
2.56-2.8213.60.08518734.0251100
2.82-3.2313.90.0618853.2241100
3.23-4.0713.70.0519163.2941100
4.07-10012.70.05120453.336199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
HKL-3000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TOT

3tot


Resolution: 1.501→27.724 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.8804 / SU ML: 0.1 / σ(F): 0 / σ(I): 0 / Phase error: 17.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1844 1841 5 %RANDOM
Rwork0.1556 ---
all0.1571 36830 --
obs0.1571 36830 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.04 Å2 / Biso mean: 27.13 Å2 / Biso min: 11.15 Å2
Refinement stepCycle: LAST / Resolution: 1.501→27.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1617 0 49 208 1874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091757
X-RAY DIFFRACTIONf_angle_d1.2952379
X-RAY DIFFRACTIONf_chiral_restr0.064257
X-RAY DIFFRACTIONf_plane_restr0.006310
X-RAY DIFFRACTIONf_dihedral_angle_d13.005678
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.501-1.54120.21861230.183726702793
1.5412-1.58650.2181250.174726242749
1.5865-1.63770.19071460.154426562802
1.6377-1.69630.20871250.15726612786
1.6963-1.76420.19061480.155426512799
1.7642-1.84440.181550.157626312786
1.8444-1.94170.17011570.150326672824
1.9417-2.06330.15751250.145826842809
2.0633-2.22250.1511500.140326832833
2.2225-2.44610.16591410.144127012842
2.4461-2.79970.15941550.148527002855
2.7997-3.52620.2161530.161327412894
3.5262-27.72880.19451380.162129203058
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)
11.17720.1819-0.25861.8935-1.41522.32090.0379-0.2050.0320.2846-0.0823-0.1539-0.23780.25260.04790.1899-0.0182-0.03620.214-0.02890.15242.266915.209832.5217
23.246-0.74760.38472.7125-1.84611.42690.1221-0.33050.16490.3734-0.04270.1649-0.53-0.2075-0.06950.23650.00060.03270.1896-0.04710.1611-8.111916.468332.1447
30.02440.2281-0.0853.38451.81055.58-0.2214-0.17890.8260.1428-0.22220.5853-0.7867-1.09130.40950.260.0998-0.02130.3034-0.06070.3119-12.012626.38322.0733
44.2798-2.07940.6354.5153-1.28573.2608-0.1429-0.19960.0346-0.00150.17710.0275-0.0057-0.0191-0.03630.1003-0.0078-0.00790.1008-0.02740.0875-3.612710.516316.3182
51.2711-0.25710.15832.6835-0.63321.109-0.0321-0.0808-0.296-0.1554-0.032-0.36790.46330.4660.06230.24810.1360.03560.283-0.01360.24156.96510.257113.7257
61.86550.00410.4111.7743-0.16032.28060.03990.1672-0.0446-0.1459-0.0424-0.13620.010.2686-0.00150.12070.01590.00430.159-0.00790.13433.731917.342811.1575
71.62651.22741.18451.66561.28435.3911-0.0360.11760.037-0.07610.0325-0.245-0.04930.63130.06520.14950.01050.0040.19830.00350.16957.722923.510415.3847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 50 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 72 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 83 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 112 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 142 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 180 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 181 through 203 )A0

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