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

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Basic information

Entry
Database: PDB / ID: 4ikh
TitleCrystal structure of a glutathione transferase family member from Pseudomonas fluorescens pf-5, target efi-900003, with two glutathione bound
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


glutathione transferase / glutathione 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, C-terminal / 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 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, C-terminal / 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
Similarity search - Component
Biological speciesPseudomonas protegens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsVetting, M.W. / Sauder, J.M. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Burley, S.K. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a glutathione transferase family member from Pseudomonas fluorescens pf-5, target efi-900003, with two glutathione bound
Authors: Vetting, M.W. / Sauder, J.M. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Burley, S.K. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionDec 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references / Structure summary
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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)28,5684
Polymers27,9181
Non-polymers6503
Water1,08160
1
A: Glutathione S-transferase
hetero molecules

A: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1368
Polymers55,8362
Non-polymers1,3006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area6850 Å2
ΔGint-69 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.189, 88.189, 159.834
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

Detailsbiological unit is dimer

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Components

#1: Protein Glutathione S-transferase


Mass: 27917.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens (bacteria) / Strain: Pf-5 / Gene: PFL_2287 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4KED9, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.21 Å3/Da / Density % sol: 61.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl + 5 mM Reduced glutathione), Reservoir (35 % v/v pentaerythritol ethoxylate (15/4 EO/OH) 0.2 M CaCl2, 0.1 M HEPES-NaOH pH 6.5), Cryoprotection ...Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl + 5 mM Reduced glutathione), Reservoir (35 % v/v pentaerythritol ethoxylate (15/4 EO/OH) 0.2 M CaCl2, 0.1 M HEPES-NaOH pH 6.5), Cryoprotection (harvested straight from drop), 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: Nov 8, 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: 2.1→79.917 Å / Num. all: 22195 / Num. obs: 22195 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.2 % / Biso Wilson estimate: 36.77 Å2 / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.2115.50.7614874931520.76100
2.21-2.3515.50.5271.44631529920.527100
2.35-2.5115.40.3652.14373528320.365100
2.51-2.7115.40.2153.54073226390.215100
2.71-2.9715.30.1644.53766524560.164100
2.97-3.3215.30.1066.43428122390.106100
3.32-3.8315.10.0994.83016319970.099100
3.83-4.7150.1055.42558717110.105100
4.7-6.6414.40.0688.91975913690.068100
6.64-39.95912.20.03915.798948080.03996.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→38.608 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8055 / SU ML: 0.19 / σ(F): 0 / σ(I): 0 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1123 5.09 %RANDOM
Rwork0.2072 ---
all0.2085 22054 --
obs0.2085 22054 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.49 Å2 / Biso mean: 49.6903 Å2 / Biso min: 20.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 41 60 1911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071911
X-RAY DIFFRACTIONf_angle_d0.9962591
X-RAY DIFFRACTIONf_chiral_restr0.071271
X-RAY DIFFRACTIONf_plane_restr0.005341
X-RAY DIFFRACTIONf_dihedral_angle_d14.801709
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.19560.32491250.28412534265999
2.1956-2.31130.30451470.24925582705100
2.3113-2.45610.30371390.229125652704100
2.4561-2.64570.26981420.21882566270899
2.6457-2.91190.27271380.211625932731100
2.9119-3.33310.24131540.216726152769100
3.3331-4.19850.20481320.186826742806100
4.1985-38.61420.19891460.19562826297299
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)
10.839-0.05710.86560.4556-0.30561.02680.0197-0.0519-0.22570.01760.0559-0.60170.2840.4438-0.11750.48510.32760.03560.71850.05940.697819.372334.175914.6816
21.40950.26860.22321.5392-0.18541.0834-0.21130.0658-0.1628-0.64540.2249-0.11890.10340.2705-0.0070.3306-0.14010.03980.3719-0.01380.27464.14345.72535.2188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 28 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 231 )A0

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