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

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Basic information

Entry
Database: PDB / ID: 4kdx
TitleCrystal structure of a glutathione transferase family member from burkholderia graminis, target efi-507264, bound gsh, ordered domains, space group p21, form(1)
ComponentsGlutathione S-transferase domain
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
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / 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 domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / 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 GstB
Similarity search - Component
Biological speciesBurkholderia graminis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 burkholderia graminis, target efi-507264, bound gsh, ordered domains, space group P21, form(1)
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 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 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 domain
B: Glutathione S-transferase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9726
Polymers52,1732
Non-polymers7994
Water8,251458
1
A: Glutathione S-transferase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3942
Polymers26,0861
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutathione S-transferase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5784
Polymers26,0861
Non-polymers4923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.844, 56.107, 67.317
Angle α, β, γ (deg.)90.00, 108.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutathione S-transferase domain /


Mass: 26086.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia graminis (bacteria) / Strain: C4D1M / Gene: BgramDRAFT_2467 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1FZ96
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 298 K / pH: 7.5
Details: Protein (10 mM Hepes, 150 mM NaCl, 5% glycerol, 5 mM GSH); Reservoir (0.2 M AmmoniumAcetate 0.1 M HEPES pH 7.5 25 %(w/v) PEG 3350); Cryoprotection (reservoir + 20% glycerol) , VAPOR ...Details: Protein (10 mM Hepes, 150 mM NaCl, 5% glycerol, 5 mM GSH); Reservoir (0.2 M AmmoniumAcetate 0.1 M HEPES pH 7.5 25 %(w/v) PEG 3350); 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
DetectorDetector: 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: 1.35→200 Å / Num. obs: 93495 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 13.64 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 19.9
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 48

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IEL

4iel


Resolution: 1.35→24.32 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.11 / σ(F): 0 / Phase error: 16.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.167 4679 5 %
Rwork0.148 --
obs0.148 93495 91.5 %
all-93495 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.54 Å2
Refinement stepCycle: LAST / Resolution: 1.35→24.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 52 458 3830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093513
X-RAY DIFFRACTIONf_angle_d1.3164782
X-RAY DIFFRACTIONf_dihedral_angle_d11.3821275
X-RAY DIFFRACTIONf_chiral_restr0.073495
X-RAY DIFFRACTIONf_plane_restr0.007635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3502-1.36560.3452690.24261543X-RAY DIFFRACTION48
1.3656-1.38160.2384950.22311667X-RAY DIFFRACTION53
1.3816-1.39850.25551180.20152015X-RAY DIFFRACTION62
1.3985-1.41620.2131110.18792300X-RAY DIFFRACTION71
1.4162-1.43480.22231390.18982510X-RAY DIFFRACTION79
1.4348-1.45450.23381370.20152776X-RAY DIFFRACTION86
1.4545-1.47530.22041620.20072949X-RAY DIFFRACTION91
1.4753-1.49730.19781560.18083051X-RAY DIFFRACTION94
1.4973-1.52070.19781280.1833100X-RAY DIFFRACTION95
1.5207-1.54560.21711660.18453052X-RAY DIFFRACTION96
1.5456-1.57220.1941720.15743150X-RAY DIFFRACTION97
1.5722-1.60080.18911520.14663099X-RAY DIFFRACTION96
1.6008-1.63160.17211450.14533112X-RAY DIFFRACTION97
1.6316-1.66490.16961560.14133172X-RAY DIFFRACTION98
1.6649-1.70110.191580.13963124X-RAY DIFFRACTION97
1.7011-1.74070.16921810.1423162X-RAY DIFFRACTION98
1.7407-1.78420.17031780.14153160X-RAY DIFFRACTION98
1.7842-1.83240.17171720.13683178X-RAY DIFFRACTION98
1.8324-1.88630.16351760.13883182X-RAY DIFFRACTION98
1.8863-1.94720.16441690.15713160X-RAY DIFFRACTION98
1.9472-2.01670.1721970.14153164X-RAY DIFFRACTION99
2.0167-2.09740.15551750.1393190X-RAY DIFFRACTION99
2.0974-2.19280.16021570.13813210X-RAY DIFFRACTION99
2.1928-2.30840.17481620.14013224X-RAY DIFFRACTION99
2.3084-2.45290.15151880.12863226X-RAY DIFFRACTION99
2.4529-2.6420.15351880.12813212X-RAY DIFFRACTION100
2.642-2.90750.14231490.14323271X-RAY DIFFRACTION100
2.9075-3.32730.15111740.14323255X-RAY DIFFRACTION100
3.3273-4.18860.15971860.13463268X-RAY DIFFRACTION100
4.1886-24.32620.16221630.16463334X-RAY DIFFRACTION99
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)
11.1014-0.381-0.54611.25960.3261.87410.01720.03330.0702-0.082-0.0188-0.1705-0.04660.1825-0.00210.0689-0.00890.010.08940.00580.077328.216421.010115.9648
21.42480.20460.24831.9334-0.23611.98210.02170.23980.0059-0.39060.07380.18450.1405-0.0807-0.05890.14240.0067-0.03970.1007-0.01370.143310.011417.45195.4981
31.35860.01790.09221.4858-0.00251.4328-0.03480.07980.211-0.18240.02960.301-0.0807-0.12650.02790.10370.0107-0.03260.08020.00850.147710.587729.49410.4541
42.8016-0.43910.99332.631-0.4422.28430.0826-0.1314-0.18080.01-0.02590.23620.1033-0.2056-0.03550.0911-0.0153-0.00520.09830.00130.13056.5766-1.537621.8619
53.4919-0.78883.64761.1203-0.22046.85610.1917-0.1254-0.3068-0.1191-0.10360.44430.3725-0.4639-0.05160.1829-0.0475-0.03410.19310.00680.2715-3.4126-1.302417.8874
62.02440.04230.92421.229-0.05551.6909-0.0021-0.11080.0341-0.00070.01270.267-0.0098-0.2368-0.00740.0872-0.00210.01320.11780.00050.12595.93488.163823.4228
71.65790.1563-0.46993.16891.26564.41830.0341-0.0621-0.04140.11620.0433-0.13630.0240.1947-0.06150.08350.00720.01060.08150.00590.086923.25239.103620.7305
82.6380.98890.53312.30780.39414.18720.19140.35040.0936-0.2158-0.17750.4460.1664-0.30470.00420.16350.0576-0.03790.1783-0.02130.172312.9632-1.52280.8775
93.0319-0.12022.71921.57570.13787.52720.04870.375-0.046-0.2422-0.0548-0.0075-0.1560.2904-0.00870.13770.04180.03510.1371-0.00680.111326.1735-0.51155.8963
101.28310.27260.25081.40170.27781.6593-0.02090.0316-0.1751-0.0455-0.0258-0.0130.24150.08810.05640.12130.02480.01420.0793-0.00030.09721.2072-7.034617.3122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 86 )
2X-RAY DIFFRACTION2chain 'A' and (resid 87 through 149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 207 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 23 )
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 41 )
6X-RAY DIFFRACTION6chain 'B' and (resid 42 through 86 )
7X-RAY DIFFRACTION7chain 'B' and (resid 87 through 102 )
8X-RAY DIFFRACTION8chain 'B' and (resid 103 through 124 )
9X-RAY DIFFRACTION9chain 'B' and (resid 125 through 149 )
10X-RAY DIFFRACTION10chain 'B' and (resid 150 through 207 )

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