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- PDB-4yh2: Glutathione Transferase E6 from Drosophila melanogaster -

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Basic information

Entry
Database: PDB / ID: 4yh2
TitleGlutathione Transferase E6 from Drosophila melanogaster
ComponentsGlutathione S transferase E6
KeywordsTRANSFERASE / Drosophila
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / 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 / 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, C-terminal domain / 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 / 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 E6
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.72 Å
AuthorsWongsantichon, J. / Robinson, R.C. / Ketterman, A.J.
Citation
Journal: Biosci.Rep. / Year: 2015
Title: Epsilon glutathione transferases possess a unique class-conserved subunit interface motif that directly interacts with glutathione in the active site
Authors: Wongsantichon, J. / Robinson, R.C. / Ketterman, A.J.
#1: Journal: Biochem.J. / Year: 2012
Title: A preliminary characterization of the cytosolic glutathione transferase proteome from Drosophila melanogaster
Authors: Saisawang, C. / Wongsantichon, J. / Ketterman, A.J.
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S transferase E6
B: Glutathione S transferase E6
C: Glutathione S transferase E6
D: Glutathione S transferase E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4008
Polymers100,1704
Non-polymers1,2294
Water17,637979
1
A: Glutathione S transferase E6
C: Glutathione S transferase E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7004
Polymers50,0852
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-29 kcal/mol
Surface area18680 Å2
MethodPISA
2
B: Glutathione S transferase E6
D: Glutathione S transferase E6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7004
Polymers50,0852
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-29 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.350, 58.860, 122.810
Angle α, β, γ (deg.)90.000, 128.250, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glutathione S transferase E6


Mass: 25042.564 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GstE6, CG17530, Dmel_CG17530 / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A1ZB71, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


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


Mass: 18.015 Da / Num. of mol.: 979 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 288 K / Method: vapor diffusion / Details: PEG3350, Sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.72→96.44 Å / Num. obs: 105003 / % possible obs: 99.8 % / Redundancy: 6.6 % / Net I/σ(I): 12.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
xia2data reduction
xia2phasing
RefinementResolution: 1.72→96.44 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 5247 5 %Random selection
Rwork0.1571 99753 --
obs0.1587 105000 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.07 Å2 / Biso mean: 25.5411 Å2 / Biso min: 8.68 Å2
Refinement stepCycle: final / Resolution: 1.72→96.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7040 0 80 979 8099
Biso mean--23.1 34.68 -
Num. residues----881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067284
X-RAY DIFFRACTIONf_angle_d1.0579904
X-RAY DIFFRACTIONf_chiral_restr0.0441123
X-RAY DIFFRACTIONf_plane_restr0.0061261
X-RAY DIFFRACTIONf_dihedral_angle_d12.6582646
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 (%)
1.72-1.73950.33231680.247932663434100
1.7395-1.760.26931670.238232923459100
1.76-1.78150.26871700.232833853555100
1.7815-1.8040.24821800.22332403420100
1.804-1.82780.2571600.221733263486100
1.8278-1.85280.26171600.203533503510100
1.8528-1.87930.2731640.202433063470100
1.8793-1.90730.22451540.200633563510100
1.9073-1.93710.24062040.184632863490100
1.9371-1.96890.20811810.179732753456100
1.9689-2.00290.21981570.174433443501100
2.0029-2.03930.20941820.175133033485100
2.0393-2.07850.21551750.172433393514100
2.0785-2.12090.211650.171433383503100
2.1209-2.16710.20431840.159333183502100
2.1671-2.21750.17771770.153432853462100
2.2175-2.27290.1951760.156733653541100
2.2729-2.33440.18981840.156232533437100
2.3344-2.40310.1772010.150533123513100
2.4031-2.48070.21281910.153733243515100
2.4807-2.56930.19431660.148533383504100
2.5693-2.67220.20161610.161333783539100
2.6722-2.79380.19861640.171633323496100
2.7938-2.94110.18721580.167433393497100
2.9411-3.12540.22241730.162733323505100
3.1254-3.36670.19581910.16223300349199
3.3667-3.70560.19511740.1483346352099
3.7056-4.24180.13711900.12673331352199
4.2418-5.34420.13481920.119133673559100
5.3442-96.59670.14491780.13113427360599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1679-0.157-0.10210.1507-0.03250.0718-0.0007-0.02290.11190.06110.03750.1064-0.1436-0.07040.0020.12150.01230.02050.111-0.01840.1652-40.6388-3.240825.1474
20.0032-0.02560.01260.0203-0.0060.00310.0573-0.2086-0.04960.20740.14350.2612-0.0006-0.1983-0.00020.2591-0.00020.06440.26770.020.2089-38.8082-14.611336.7596
30.03-0.0303-0.03220.0491-0.00720.0855-0.0559-0.0569-0.10810.0117-0.00060.17840.1328-0.1242-00.1506-0.01540.02490.1655-0.01360.1823-38.8898-14.46725.8728
40.14730.05740.02650.47980.1020.0830.0370.2727-0.0485-0.04-0.06160.20340.08550.0482-0.02140.13060.0087-0.02370.2131-0.03950.1428-37.3379-9.006410.4495
50.06370.039-0.01980.1256-0.03480.01950.09440.17730.00170.0165-0.1-0.002-0.04880.05410.0040.13440.0173-0.01070.20020.00010.1179-24.6223-8.775910.848
60.02790.01190.00120.06890.01160.0224-0.078-0.0758-0.05960.21520.0366-0.07950.0554-0.0177-0.00250.2236-0.0084-0.0250.1875-0.0220.1408-20.0768-3.692834.3988
70.06050.018-0.04360.03630.0010.0260.07370.02570.16630.0585-0.007-0.2509-0.05870.27810.00010.1612-0.025-0.02030.2180.00720.2331-13.40371.007521.8927
80.1087-0.14060.06530.1677-0.06240.01930.01590.16040.29220.0029-0.0689-0.0645-0.01660.049-0.00010.1417-0.0141-0.00230.18510.04520.2046-23.38434.166815.6007
90.03510.02780.09350.12760.2010.3691-0.11020.13040.38110.0222-0.0456-0.0166-0.2046-0.0456-0.06450.17730.0009-0.00480.14740.05930.2671-30.43878.966315.8346
100.04450.1022-0.08440.2225-0.21330.1625-0.0751-0.04150.38090.19460.1343-0.0151-0.12590.21850.04020.22860.0231-0.04830.1884-0.08990.2765-24.04846.877234.4903
110.0181-0.03240.00170.04790.03040.03010.0296-0.00490.1321-0.03180.00480.2328-0.0567-0.034-00.13990.0142-0.00990.1280.01930.155313.7167.836426.5699
120.18430.0451-0.19350.12760.08620.5308-0.06710.14280.079-0.13930.00420.1707-0.0399-0.2793-0.02760.13050.0095-0.03430.21240.0170.20538.54631.111121.1866
130.1419-0.0654-0.0160.17180.0040.0801-0.00020.05590.1515-0.0605-0.0003-0.0063-0.0335-0.039300.1436-0.0069-0.01360.1470.04250.15623.87566.824220.3559
140.0793-0.1760.01950.33650.19880.3322-0.01290.00940.11780.0057-0.01810.11060.0798-0.10720.00010.1204-0.02180.0120.111-0.00520.104819.2275-5.691735.9426
150.068-0.0679-0.00140.0490.00380.0503-0.0285-0.157-0.18790.18690.0388-0.11280.04470.0993-0.00030.22680.00080.03370.1560.00150.142522.4374-5.881546.4295
160.01710.00820.00860.0006-0.0080.0168-0.09350.08950.20990.0999-0.0979-0.2531-0.28910.21970.00020.1918-0.0315-0.04190.1485-0.0110.160732.3029.317239.3961
170.01120.0694-0.02050.10460.04780.0489-0.02160.00170.14840.0311-0.04050.0274-0.0099-0.09840.00180.1475-0.02160.01620.1236-0.02090.124719.42313.106443.5464
180.0475-0.0016-0.05060.07550.02890.05480.049-0.05290.0820.18120.02930.1562-0.1032-0.02260.00030.1913-0.00410.02990.1385-0.00450.164120.048512.938740.7954
190.0243-0.0027-0.04080.03290.05080.0837-0.0468-0.03360.02440.0223-0.01130.22520.0116-0.2794-0.00060.1858-0.00020.08730.2479-0.01910.33545.8965-0.258943.383
200.0675-0.0087-0.05880.085-0.02520.16630.06380.311-0.1601-0.0091-0.2057-0.04470.08650.1648-0.21540.15220.0754-0.00140.2659-0.06880.0871-13.4734-22.979410.0308
210.05360.0703-0.08370.04260.05780.0819-0.01750.5450.44570.1407-0.4226-0.5086-0.0630.6236-0.10790.07480.07680.11170.4246-0.057-0.0746-7.8256-14.67718.9963
220.015-0.021-0.00350.02860.01190.01990.04710.2048-0.0085-0.099-0.01810.11320.03770.1043-0.02480.2080.01320.00740.35350.00270.101-15.8618-13.33363.1428
230.03750.00060.00690.04680.03590.03570.11130.1514-0.00910.0128-0.11920.14630.0751-0.03910.00010.16510.0391-0.02870.2597-0.07030.1359-27.8048-21.51476.548
240.0819-0.26760.06030.2418-0.0329-0.0131-0.05050.05090.07820.0337-0.06980.0137-0.04360.0748-0.00080.13-0.0136-0.00580.14030.00360.0964-18.3433-15.732524.4939
250.0513-0.0332-0.01410.0522-0.04770.0443-0.0306-0.2433-0.09290.0795-0.01710.0761-0.0798-0.0705-0.00010.19870.0005-0.0110.1670.01120.1445-21.4638-20.557434.1291
260.06460.042-0.03470.1910.00830.0730.11060.0381-0.20470.0037-0.05230.01950.14250.07720.00030.1958-0.0133-0.01820.1533-0.01490.1881-23.7624-28.180424.7884
270.0544-0.01040.0572-0.00990.00110.05540.08930.0089-0.3460.0425-0.04450.07230.21110.1490.00510.23920.0308-0.02030.1816-0.05580.2548-20.4724-34.256919.9173
280.0364-0.0031-0.01050.0918-0.0740.04610.1451-0.0844-0.14790.0106-0.0801-0.19830.05320.1659-0.0010.17760.0469-0.01990.2222-0.00890.1933-5.4822-24.525128.6851
290.0975-0.0893-0.01240.0732-0.02530.05680.04050.0257-0.07140.0895-0.0472-0.1162-0.03720.02780.0010.1423-0.0172-0.00530.0930.00980.165641.2231-14.73228.4158
300.2239-0.04130.00620.11290.02210.03140.043-0.1838-0.14050.1163-0.0384-0.20490.02380.0042-0.00010.1911-0.014-0.03590.19090.04920.21340.4855-13.70438.4407
310.13070.07-0.00890.18310.02840.1085-0.02140.03160.09280.032-0.0164-0.1467-0.04310.0153-0.00010.1372-0.009-0.00610.10860.01360.136439.8619-4.219525.0165
320.2216-0.0265-0.01520.21010.15250.06640.06840.0372-0.01540.1254-0.06430.0302-0.0730.0365-0.00690.1479-0.02350.00340.08890.00160.113423.2643-14.055930.6931
330.0454-0.01390.0340.054-0.0020.0147-0.01880.0684-0.0641-0.04610.07670.2383-0.0218-0.25610.00060.1429-0.02380.01430.1598-0.00210.170914.6815-18.944725.1536
340.02310.0030.01320.0071-0.01490.002-0.05270.36220.1768-0.24830.00560.07770.0005-0.0277-0.00010.2071-0.0063-0.01190.2446-0.00080.140926.2203-11.751710.9406
350.00050.0087-0.07310.00920.0010.0524-0.05840.1156-0.073-0.05910.0514-0.08250.0854-0.0315-00.1497-0.02020.0020.1432-0.01580.134823.7489-21.579221.8375
360.0979-0.07630.03930.24780.01070.15390.01010.1042-0.254-0.0394-0.0049-0.03850.1095-0.0216-0.00050.1774-0.01070.00430.1295-0.01840.185629.2273-25.759623.7461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 38 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 49 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 67 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 89 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 104 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 105 through 128 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 129 through 145 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 146 through 182 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 183 through 202 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 203 through 222 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 24 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 25 through 56 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 57 through 89 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 90 through 128 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 129 through 145 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 146 through 158 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 159 through 182 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 183 through 202 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 203 through 221 )B0
20X-RAY DIFFRACTION20chain 'C' and (resid 3 through 24 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 25 through 56 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 57 through 67 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 68 through 89 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 90 through 128 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 129 through 145 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 146 through 182 )C0
27X-RAY DIFFRACTION27chain 'C' and (resid 183 through 202 )C0
28X-RAY DIFFRACTION28chain 'C' and (resid 203 through 222 )C0
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 24 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 25 through 56 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 57 through 89 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 90 through 128 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 129 through 145 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 146 through 158 )D0
35X-RAY DIFFRACTION35chain 'D' and (resid 159 through 182 )D0
36X-RAY DIFFRACTION36chain 'D' and (resid 183 through 221 )D0

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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