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- PDB-4kf9: Crystal structure of a glutathione transferase family member from... -

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Basic information

Entry
Database: PDB / ID: 4kf9
TitleCrystal structure of a glutathione transferase family member from ralstonia solanacearum, target efi-501780, with bound gsh coordinated to a zinc ion, ordered active site
ComponentsGlutathione s-transferase protein
KeywordsTRANSFERASE / glutathione S-transferase fold / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


Glutaredoxin - #110 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutaredoxin / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GLUTATHIONE
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 ralstonia solanacearum, target efi-501780, with bound gsh coordinated to a zinc ion, ordered active site
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 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 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 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5309
Polymers35,7841
Non-polymers7468
Water4,540252
1
A: Glutathione s-transferase protein
hetero molecules

A: Glutathione s-transferase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,06018
Polymers71,5682
Non-polymers1,49216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area6970 Å2
ΔGint-217 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.527, 111.527, 98.977
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

21A-715-

HOH

Detailsbiological unit is dimer

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Components

#1: Protein Glutathione s-transferase protein


Mass: 35783.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Gene: gstG, RSIPO_01298 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: glutathione transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 4.97 Å3/Da / Density % sol: 75.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Protein (10 mM Hepes pH 7.5, 5 mM GSH), Reservoir (0.2 M Zinc Acetate, 0.1 M Sodium Acetate pH 4.5, 10 %(w/v) PEG 3000), 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 225 HE / Detector: CCD / Date: Apr 6, 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: 2.3→96.585 Å / Num. all: 32015 / Num. obs: 32015 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 39.78 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.425.70.8020.92627846100.802100
2.42-2.577.30.5371.43216143840.537100
2.57-2.757.60.3432.23100441020.343100
2.75-2.977.60.2263.32900338400.226100
2.97-3.257.50.1335.52678535530.133100
3.25-3.647.50.08482424732190.084100
3.64-4.27.50.0768.12134928510.076100
4.2-5.147.40.1135.21820224440.113100
5.14-7.277.30.1045.81397719050.104100
7.27-48.2926.70.0579.7740311070.05799.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IC8

3ic8


Resolution: 2.3→48.293 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8922 / SU ML: 0.2 / σ(F): 0 / σ(I): 0 / Phase error: 17.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 1616 5.05 %RANDOM
Rwork0.1594 ---
all0.1608 31979 --
obs0.1608 31979 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.7 Å2 / Biso mean: 32.3942 Å2 / Biso min: 11.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2439 0 36 252 2727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142581
X-RAY DIFFRACTIONf_angle_d1.0813524
X-RAY DIFFRACTIONf_chiral_restr0.065389
X-RAY DIFFRACTIONf_plane_restr0.005461
X-RAY DIFFRACTIONf_dihedral_angle_d13.381928
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.36780.24421260.227325272653100
2.3678-2.44420.25991420.203724762618100
2.4442-2.53160.21381220.187625102632100
2.5316-2.63290.17781340.167924782612100
2.6329-2.75270.21231440.156925242668100
2.7527-2.89790.18421260.156624982624100
2.8979-3.07940.19961380.160725242662100
3.0794-3.31710.17951280.1625292657100
3.3171-3.65080.16141330.148925252658100
3.6508-4.17880.16791410.137925402681100
4.1788-5.26390.15291460.140625652711100
5.2639-48.30320.21721360.17682667280399
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)
10.21810.003-0.20750.2202-0.19180.34760.05420.0231-0.2002-0.0354-0.217-0.01910.29-0.1771-0.0250.2533-0.07190.02460.1641-0.03440.23649.7327-24.9382-17.0493
20.13630.002-0.11290.09530.0270.0690.1589-0.0245-0.0774-0.0227-0.20320.02790.3577-0.011-0.00030.24340.03580.01560.19840.01160.247761.6024-23.6424-21.6095
30.3218-0.32840.33260.3778-0.37820.37790.03530.07880.2878-0.2154-0.23610.28860.0846-0.2053-0.09730.2059-0.0213-0.0060.2135-0.08550.217843.3462-16.348-24.0238
40.44360.1916-0.1980.54290.05370.74190.085-0.18880.14640.0989-0.35040.0620.2806-0.2173-0.33860.175-0.07370.01480.16440.0150.122155.6477-9.1279-8.0957
50.0659-0.1505-0.09130.6548-0.15880.859-0.1004-0.19530.23640.0112-0.0515-0.33150.19830.3484-0.01620.1488-0.0382-0.02930.27310.07730.24969.793-14.1172-8.292
60.1578-0.240.02480.50620.01540.41620.0326-0.06440.02630.2733-0.20630.22990.1011-0.1715-0.03760.1781-0.07480.05440.1998-0.05140.192245.4208-7.9836-4.7368
70.5883-0.17070.47680.74510.48170.88210.2121-0.1337-0.2901-0.0498-0.22970.31890.7003-0.23140.06180.46610.03620.05020.0249-0.03780.292254.3968-33.8995-21.648
80.3150.10510.03630.45120.18870.68830.08970.18160.0689-0.2001-0.1716-0.08110.04150.1656-0.12510.23650.08110.06210.1799-0.01920.154160.6117-16.35-34.3713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 35 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 67 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 86 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 126 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 127 through 150 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 151 through 222 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 223 through 241 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 242 through 319 )A0

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