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- PDB-4kh7: Crystal structure of a glutathione transferase family member from... -

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Basic information

Entry
Database: PDB / ID: 4kh7
TitleCrystal structure of a glutathione transferase family member from salmonella enterica ty2, target efi-507262, with bound glutathione
ComponentsGlutathione s-transferase family protein
KeywordsTRANSFERASE / GST / glutathione S-transferase fold / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


transferase activity
Similarity search - Function
Glutathione S-transferase, N-terminal domain / 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 / 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, N-terminal domain / 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 / 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 / Glutathione S-transferase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 Salmonella enterica ty2, target efi-507262, with bound glutathione
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
DepositionApr 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 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 family protein
B: Glutathione s-transferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1604
Polymers52,5462
Non-polymers6152
Water10,881604
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glutathione s-transferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5802
Polymers26,2731
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Glutathione s-transferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5802
Polymers26,2731
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.078, 72.692, 82.896
Angle α, β, γ (deg.)90.000, 96.150, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a dimer

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Components

#1: Protein Glutathione s-transferase family protein


Mass: 26272.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Strain: subsp. enterica serovar Typhi str. Ty2 / Gene: yliJ, t2034 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Z859
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


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


Mass: 18.015 Da / Num. of mol.: 604 / 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: 3.03 Å3/Da / Density % sol: 59.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM GSH), Reservoir (0.1 M Bis-Tris Propane pH 7, 1.2 M Potassium Sodium Tartrate Tetrahydrate), Cryoprotection (reservoir + 20% ...Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM GSH), Reservoir (0.1 M Bis-Tris Propane pH 7, 1.2 M Potassium Sodium Tartrate Tetrahydrate), Cryoprotection (reservoir + 20% glycerol), 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: Apr 17, 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: 1.5→82.418 Å / Num. all: 99706 / Num. obs: 99706 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 15.85 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.583.70.651.253532145640.65100
1.58-1.683.70.4231.950817137530.423100
1.68-1.793.70.268348221129890.268100
1.79-1.943.70.1714.644972120630.17199.9
1.94-2.123.70.0948.341735111760.09499.9
2.12-2.373.70.06312.23726399990.06399.7
2.37-2.743.70.04416.53297588680.04499.6
2.74-3.353.70.03320.22751474760.03399
3.35-4.743.60.02327.82075357200.02397.7
4.74-72.6923.50.0231.71087430980.0294.5

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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: 4IEL

4iel


Resolution: 1.5→36.346 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.8671 / SU ML: 0.16 / σ(F): 0 / σ(I): 0 / Phase error: 20.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 4974 4.99 %RANDOM
Rwork0.1706 ---
all0.1714 99661 --
obs0.1714 99661 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.84 Å2 / Biso mean: 23.8735 Å2 / Biso min: 7.52 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 40 604 4004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013557
X-RAY DIFFRACTIONf_angle_d1.2484856
X-RAY DIFFRACTIONf_chiral_restr0.069521
X-RAY DIFFRACTIONf_plane_restr0.008637
X-RAY DIFFRACTIONf_dihedral_angle_d12.8681307
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 (%)
1.5-1.5170.33331740.293131753349100
1.517-1.53490.29291650.278331533318100
1.5349-1.55360.26051690.272931073276100
1.5536-1.57330.2741530.250531843337100
1.5733-1.5940.26831510.253931683319100
1.594-1.61580.27541420.24231893331100
1.6158-1.63890.29581530.232831633316100
1.6389-1.66340.23741820.215831753357100
1.6634-1.68940.25921550.207531303285100
1.6894-1.71710.23611770.204231463323100
1.7171-1.74670.221700.204731593329100
1.7467-1.77840.22671390.204432283367100
1.7784-1.81260.22361720.194231313303100
1.8126-1.84960.24921530.18931413294100
1.8496-1.88980.18261680.187531713339100
1.8898-1.93380.19321680.185531683336100
1.9338-1.98220.20111570.182231563313100
1.9822-2.03570.19331880.165931813369100
2.0357-2.09560.17461770.157931463323100
2.0956-2.16330.16951600.16131553315100
2.1633-2.24060.1821870.160731663353100
2.2406-2.33030.181640.1523142330699
2.3303-2.43630.19861720.160731653337100
2.4363-2.56470.17761850.15273148333399
2.5647-2.72540.17321590.151431583317100
2.7254-2.93570.18241590.14973185334499
2.9357-3.2310.19651720.1583150332299
3.231-3.69810.14791460.14633160330698
3.6981-4.65770.13521660.13243120328697
4.6577-36.35670.17111910.18623067325894

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