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

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Basic information

Entry
Database: PDB / ID: 4kgi
TitleCrystal structure of a glutathione transferase family member from Shigella flexneri, target EFI-507258, bound GSH, TEV-his-tag linker in active site
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / GST / glutathione S-transferase fold / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutaredoxin / Glutaredoxin / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 Shigella flexneri, target EFI-507258, bound GSH, TEV-His-tag linker in 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 29, 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
B: Glutathione S-transferase
C: Glutathione S-transferase
D: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0588
Polymers101,8284
Non-polymers1,2294
Water12,665703
1
A: Glutathione S-transferase
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5294
Polymers50,9142
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-25 kcal/mol
Surface area17200 Å2
MethodPISA
2
C: Glutathione S-transferase
D: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5294
Polymers50,9142
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-24 kcal/mol
Surface area18540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.849, 63.964, 64.238
Angle α, β, γ (deg.)94.410, 103.230, 92.110
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glutathione S-transferase


Mass: 25457.064 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 2a str. 2457T / Gene: gst, SF2457T_2570 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E3Y3H4, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / 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 / Method: sitting drop vapor diffusion / pH: 7.5
Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM GSH); Reservoir (25 % v/v Jeffamine SD2001 0.1 M sodium malonate, 0.1 M MES-NaOH pH 5.5); Cryoprotection (reservoir + 20% ...Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM GSH); Reservoir (25 % v/v Jeffamine SD2001 0.1 M sodium malonate, 0.1 M MES-NaOH pH 5.5); Cryoprotection (reservoir + 20% diethylene glycol), sitting drop vapor diffusion, 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 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: 1.6→63.675 Å / Num. all: 111907 / Num. obs: 111907 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 9.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5420 / % possible all: 93.5

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Processing

Software
NameVersionClassificationNB
SCALA0.1.27data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N2A

1n2a


Resolution: 1.6→26.267 Å / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.8636 / SU ML: 0.16 / σ(F): 0 / σ(I): 0 / Phase error: 21.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.21 5606 5.01 %RANDOM
Rwork0.1759 ---
all0.1776 111796 --
obs0.1776 111796 94.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.01 Å2 / Biso mean: 26.3971 Å2 / Biso min: 6.4 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 80 703 7299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116813
X-RAY DIFFRACTIONf_angle_d1.3219241
X-RAY DIFFRACTIONf_chiral_restr0.0781022
X-RAY DIFFRACTIONf_plane_restr0.0071192
X-RAY DIFFRACTIONf_dihedral_angle_d12.7092543
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 (%)
1.6-1.61820.30131680.26343451361993
1.6182-1.63720.29151920.25323468366093
1.6372-1.65720.26781870.23583537372494
1.6572-1.67820.24662070.22973435364294
1.6782-1.70020.27012000.22513506370694
1.7002-1.72350.28581880.21663502369094
1.7235-1.74820.24421910.2093491368294
1.7482-1.77420.25391730.19913556372994
1.7742-1.8020.22991840.19413510369495
1.802-1.83150.26191850.19743547373295
1.8315-1.86310.21471820.1893520370295
1.8631-1.89690.21111770.18023547372495
1.8969-1.93340.23971930.18893555374895
1.9334-1.97290.21311880.18793519370795
1.9729-2.01570.21851750.18593578375396
2.0157-2.06260.21441870.17713607379496
2.0626-2.11420.1961800.17843520370095
2.1142-2.17130.23771930.17453593378696
2.1713-2.23520.2152170.16623558377596
2.2352-2.30730.20191760.16823605378196
2.3073-2.38970.1811980.15933556375496
2.3897-2.48530.21431770.16513624380196
2.4853-2.59830.18691970.1613566376397
2.5983-2.73520.20132100.16333610382097
2.7352-2.90630.19551900.16993654384497
2.9063-3.13040.22031970.17673575377297
3.1304-3.44480.20221920.16763640383297
3.4448-3.94180.1951750.16023611378697
3.9418-4.96080.17951690.15223536370594
4.9608-26.27050.19651580.19383213337186
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)
12.1323-0.36740.37271.3135-1.19142.6459-0.01590.00160.21280.0739-0.0622-0.2035-0.14930.18180.06750.0687-0.02530.01310.09440.00450.12369.12880.632810.0127
22.55340.28630.15371.46480.12111.2711-0.00940.49020.1686-0.26340.04230.0334-0.05550.0895-0.02780.1148-0.00540.01270.19080.0440.0677-4.1801-0.2848-4.4034
32.12420.24790.2770.63660.87223.0452-0.03670.07480.2295-0.0603-0.09380.1656-0.1355-0.31430.10.07340.02660.00880.1132-0.00640.1266-27.59431.37854.4485
42.7017-0.55710.16991.8207-0.01411.2244-0.0511-0.4650.08360.28920.1057-0.00320.0136-0.0503-0.03010.11090.00490.00610.1581-0.01480.0649-14.2509-2.3418.4125
51.40440.7814-0.62691.9365-0.70591.4105-0.01760.14470.1356-0.22220.0166-0.2710.01890.2003-0.01450.13320.00810.02220.17360.03340.154435.3002-17.4728-44.5647
63.9228-1.1922-0.70474.06180.8363.9877-0.09020.1634-0.3241-0.31-0.0349-0.67050.50230.93120.01680.24330.09380.03280.32960.00850.318542.2477-26.276-38.945
71.81670.37250.19341.6508-0.44021.92470.06080.0483-0.061-0.0208-0.049-0.01320.14090.0568-0.00310.10430.0146-0.01840.079-0.00940.083924.3996-21.6938-31.3451
84.0153-3.9892-0.09958.063-0.06151.89490.0093-0.127-0.67460.285-0.02250.24920.6658-0.10430.03680.3289-0.0348-0.03740.13650.03780.283715.9709-38.9568-32.5691
93.96442.91271.10766.16790.8725.3586-0.5418-0.12691.10260.0361-0.11350.7462-0.8518-0.76550.42580.26580.0516-0.12530.2232-0.01050.320610.7139-17.4136-36.2738
101.9657-0.3806-0.01591.5422-0.15091.40120.0060.2989-0.1118-0.1804-0.0140.20890.0808-0.0330.0120.1645-0.0134-0.04260.1201-0.00480.118717.802-26.3814-44.0932
113.7239-4.7887-2.33387.89813.78972.1472-0.0695-0.07-0.0420.3031-0.07370.4920.0675-0.23750.12530.1879-0.04680.05950.2874-0.01690.216113.9657-20.5236-6.7734
121.64540.1844-0.35093.66291.35232.12680.1029-0.43790.10780.3469-0.13990.1350.1471-0.20120.03820.1446-0.00610.00120.2362-0.05150.101623.0709-20.594-8.1352
133.58270.6991-0.16443.7576-0.04872.90470.0462-0.2281-0.29690.2071-0.11860.58190.5041-0.63430.03730.2641-0.07920.02310.2764-0.03510.22814.5744-25.517-15.3198
142.74390.3386-2.92660.6361-0.58463.18580.0139-0.4030.4769-0.0757-0.09130.1204-0.29480.57480.040.1536-0.0169-0.01640.155-0.05910.186831.9738-8.6324-18.0222
151.8598-0.68990.2577.018-0.71542.1270.06830.12030.0451-0.0039-0.1016-0.22060.11340.24360.01960.11440.0136-0.02370.1403-0.01630.097634.3106-21.2578-25.3539
162.33730.5540.39973.80080.32842.27530.05940.1062-0.8737-0.00450.247-0.18380.74280.0932-0.24310.41970.0436-0.05870.1877-0.02930.331533.6662-39.745-22.1928
172.6867-1.95860.42278.4604-1.16024.1874-0.65710.13280.9192-0.04960.0683-0.9392-0.91370.8090.48960.301-0.0182-0.12950.3317-0.03250.301443.4214-18.9597-15.765
181.97950.783-0.23541.69380.33382.3050.0778-0.3489-0.26630.2340.0443-0.32480.29190.0862-0.08280.2180.0399-0.06810.1812-0.00180.142836.5211-29.5146-9.5995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 65 )A1 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 200 )A66 - 200
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 65 )B1 - 65
4X-RAY DIFFRACTION4chain 'B' and (resid 66 through 200 )B66 - 200
5X-RAY DIFFRACTION5chain 'C' and (resid -5 through 29 )C-5 - 29
6X-RAY DIFFRACTION6chain 'C' and (resid 30 through 65 )C30 - 65
7X-RAY DIFFRACTION7chain 'C' and (resid 66 through 118 )C66 - 118
8X-RAY DIFFRACTION8chain 'C' and (resid 119 through 139 )C119 - 139
9X-RAY DIFFRACTION9chain 'C' and (resid 140 through 152 )C140 - 152
10X-RAY DIFFRACTION10chain 'C' and (resid 153 through 200 )C153 - 200
11X-RAY DIFFRACTION11chain 'D' and (resid -5 through 9 )D-5 - 9
12X-RAY DIFFRACTION12chain 'D' and (resid 10 through 29 )D10 - 29
13X-RAY DIFFRACTION13chain 'D' and (resid 30 through 76 )D30 - 76
14X-RAY DIFFRACTION14chain 'D' and (resid 77 through 88 )D77 - 88
15X-RAY DIFFRACTION15chain 'D' and (resid 89 through 104 )D89 - 104
16X-RAY DIFFRACTION16chain 'D' and (resid 105 through 140 )D105 - 140
17X-RAY DIFFRACTION17chain 'D' and (resid 141 through 152 )D141 - 152
18X-RAY DIFFRACTION18chain 'D' and (resid 153 through 200 )D153 - 200

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