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- PDB-3vk9: Crystal structure of delta-class glutathione transferase from silkmoth -

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Basic information

Entry
Database: PDB / ID: 3vk9
TitleCrystal structure of delta-class glutathione transferase from silkmoth
ComponentsGlutathione S-transferase delta
KeywordsTRANSFERASE / glutathione binding
Function / homology
Function and homology information


glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutaredoxin domain profile. / 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 / 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, N-terminal domain / Glutaredoxin domain profile. / 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 / 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 S-transferase delta
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsKakuta, Y. / Usuda, K. / Higashiura, A. / Suzuki, M. / Nakagawa, A. / Kimura, M. / Yamamoto, K.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: Structural basis for catalytic activity of a silkworm Delta-class glutathione transferase
Authors: Yamamoto, K. / Usuda, K. / Kakuta, Y. / Kimura, M. / Higashiura, A. / Nakagawa, A. / Aso, Y. / Suzuki, M.
History
DepositionNov 10, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 delta
B: Glutathione S-transferase delta
C: Glutathione S-transferase delta
D: Glutathione S-transferase delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,76012
Polymers97,0234
Non-polymers7378
Water6,774376
1
A: Glutathione S-transferase delta
hetero molecules

A: Glutathione S-transferase delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6964
Polymers48,5122
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3770 Å2
ΔGint-18 kcal/mol
Surface area17900 Å2
MethodPISA
2
B: Glutathione S-transferase delta
hetero molecules

B: Glutathione S-transferase delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,24810
Polymers48,5122
Non-polymers7378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3690 Å2
ΔGint-19 kcal/mol
Surface area17760 Å2
MethodPISA
3
C: Glutathione S-transferase delta
D: Glutathione S-transferase delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7885
Polymers48,5122
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-18 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.393, 162.184, 86.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-244-

HOH

21B-243-

HOH

31B-347-

HOH

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Components

#1: Protein
Glutathione S-transferase delta


Mass: 24255.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: GST delta / Production host: Escherichia coli (E. coli) / References: UniProt: Q60GK5, glutathione transferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.001→32.1 Å / Num. obs: 60864 / Biso Wilson estimate: 18.66 Å2

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→31.449 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8295 / SU ML: 0.62 / σ(F): 1.34 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 3057 5.03 %
Rwork0.1885 --
obs0.1913 60818 99.23 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.828 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 110.64 Å2 / Biso mean: 23.3804 Å2 / Biso min: 5.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.1527 Å20 Å20 Å2
2---0.567 Å2-0 Å2
3---0.4143 Å2
Refinement stepCycle: LAST / Resolution: 2.001→31.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6786 0 48 376 7210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087116
X-RAY DIFFRACTIONf_angle_d1.0349675
X-RAY DIFFRACTIONf_chiral_restr0.0721083
X-RAY DIFFRACTIONf_plane_restr0.0051230
X-RAY DIFFRACTIONf_dihedral_angle_d13.4072690
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.001-2.03230.32941300.23282572270298
2.0323-2.06560.29351430.236526222765100
2.0656-2.10120.29911570.23825752732100
2.1012-2.13940.31471460.211226062752100
2.1394-2.18060.28331290.215926312760100
2.1806-2.22510.27641480.209925942742100
2.2251-2.27340.27481150.206126312746100
2.2734-2.32630.25971330.194626262759100
2.3263-2.38450.24861580.193826102768100
2.3845-2.44890.29151340.184526112745100
2.4489-2.52090.23071260.192526532779100
2.5209-2.60230.28051520.19526032755100
2.6023-2.69520.25771500.200826222772100
2.6952-2.80310.251470.19452627277499
2.8031-2.93060.24821330.203526212754100
2.9306-3.08490.26011450.190226202765100
3.0849-3.2780.25231410.18972632277399
3.278-3.53080.22561360.17612634277099
3.5308-3.88560.22041460.16792622276898
3.8856-4.44650.18891390.15612643278298
4.4465-5.59690.19541280.15612671279998
5.5969-31.45260.20481210.18932735285696
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)
10.9244-0.32490.21040.9554-1.46392.9739-0.0037-0.05480.04440.1635-0.0393-0.0982-0.09190.11950.02540.08750.0008-0.01530.1064-0.01160.080317.872960.231924.4621
20.80680.0041-0.00081.25270.34750.98090.03650.0553-0.0626-0.11680.008-0.10020.07070.0453-0.03670.07180.0054-0.00350.10030.00610.04685.377556.46089.9979
31.92621.1272-0.28211.0685-1.52694.57660.03770.14830.0948-0.0924-0.1328-0.13440.10510.23450.04880.0918-0.00180.05790.15140.02180.206917.292-19.934224.8617
40.41590.501-0.26081.3084-1.62952.5998-0.02090.20380.0897-0.0565-0.233-0.2294-0.01440.35870.16550.1474-0.01970.00620.18970.07790.264322.3726-18.587821.4725
51.31740.5779-0.12242.2169-1.36323.4327-0.09390.0747-0.1105-0.17620.0335-0.0487-0.01950.1530.04710.10220.00980.08180.14520.04430.2615.5776-16.700612.0869
61.4177-0.1867-0.33450.094-0.04640.8525-0.032-0.1386-0.0126-0.014-0.1357-0.03480.187-0.00590.03910.1288-0.02830.03780.12110.0050.2286.5985-30.233724.8275
70.48590.58950.28881.3638-0.05050.83430.0648-0.13310.23870.1316-0.07230.14510.0292-0.13940.10470.0806-0.01530.06430.1561-0.06210.2939-2.4414-22.011828.058
80.95720.90140.51241.1530.28110.4121-0.05420.01620.5536-0.0534-0.06180.0316-0.23440.1504-0.02360.2152-0.06190.04390.2109-0.02910.84096.3882-1.040127.4684
90.37450.0307-0.05170.5723-0.15550.09650.1006-0.12030.42180.0806-0.05960.2007-0.10330.01-0.08110.1887-0.04070.15740.2411-0.28670.6695-2.7817-5.860735.7898
100.3980.38320.38330.64140.2420.44270.1502-0.45710.61030.3038-0.14640.06160.0012-0.12020.07190.1662-0.05730.12410.264-0.14610.3955.5134-16.137539.5199
111.63580.86130.09135.668-0.88141.09690.0557-0.03950.55210.1712-0.1219-0.0568-0.11010.04670.05650.15430.00040.04810.169-0.03960.344319.0788-10.200533.54
122.2631-0.0864-0.56782.5037-0.56333.05770.0013-0.1052-0.1943-0.08960.0107-0.04260.2010.0623-0.00370.09260.0118-0.00220.0531-0.02090.105540.42981.322121.2056
134.62031.0497-1.00562.78330.05152.98320.0907-0.2304-0.17270.4957-0.0660.05010.14190.0652-0.03880.1480.02080.02390.10650.03260.121436.80815.798731.8595
141.6848-0.0473-0.01641.1879-0.27041.3114-0.06450.0529-0.053-0.05260.0329-0.1609-0.03320.23970.01320.09780.00190.00080.11070.00050.109547.31517.681417.3677
153.41471.6295-0.04723.7538-0.52192.0919-0.0542-0.0758-0.31750.1904-0.07490.14970.2173-0.23670.16320.1613-0.04010.06360.1612-0.0040.14621.689314.173915.0107
166.73990.4915-1.83461.66120.44511.83070.04390.25270.2493-0.13640.01460.2356-0.2518-0.1626-0.06620.122-0.0017-0.03060.13450.0090.087726.347422.64096.6048
171.65980.6158-0.30231.1373-0.52521.19760.02740.1185-0.0094-0.1720.0173-0.01720.08430.0843-0.02120.09680.01220.01410.07840.00020.04140.173415.11456.5667
182.57180.1845-0.3921.604-0.55641.6533-0.06140.1704-0.2327-0.37170.07430.08210.2422-0.1952-0.00620.1491-0.02210.00620.1381-0.02540.080633.865613.03890.663
194.22660.3249-2.60131.8329-0.67282.77960.02420.334-0.4314-0.0720.05760.11680.3223-0.2246-0.00780.2030.00460.00180.065-0.01920.08630.31370.804210.5188
202.1257-0.26830.77492.2954-0.15232.112-0.02480.20750.1223-0.33340.0307-0.0572-0.0418-0.0198-0.02970.1501-0.0098-0.01910.10790.0030.089638.556138.427916.6792
211.40970.1635-0.44861.1726-0.02611.24050.0067-0.0992-0.00770.14170.027-0.0135-0.0619-0.0529-0.03280.10590.0155-0.02580.07980.01070.051434.896725.074832.0185
224.532-1.17642.86762.8705-0.54143.6064-0.0481-0.33130.43010.06510.12620.1069-0.3868-0.211-0.02960.21830.02170.01120.0849-0.00960.106729.412240.720331.8409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 1:66)A1 - 66
2X-RAY DIFFRACTION2chain A and (resseq 67:214)A67 - 214
3X-RAY DIFFRACTION3chain B and (resseq 2:23)B2 - 23
4X-RAY DIFFRACTION4chain B and (resseq 24:38)B24 - 38
5X-RAY DIFFRACTION5chain B and (resseq 39:66)B39 - 66
6X-RAY DIFFRACTION6chain B and (resseq 67:88)B67 - 88
7X-RAY DIFFRACTION7chain B and (resseq 89:104)B89 - 104
8X-RAY DIFFRACTION8chain B and (resseq 105:125)B105 - 125
9X-RAY DIFFRACTION9chain B and (resseq 126:142)B126 - 142
10X-RAY DIFFRACTION10chain B and (resseq 143:191)B143 - 191
11X-RAY DIFFRACTION11chain B and (resseq 192:214)B192 - 214
12X-RAY DIFFRACTION12chain C and (resseq 1:37)C1 - 37
13X-RAY DIFFRACTION13chain C and (resseq 38:66)C38 - 66
14X-RAY DIFFRACTION14chain C and (resseq 67:104)C67 - 104
15X-RAY DIFFRACTION15chain C and (resseq 105:125)C105 - 125
16X-RAY DIFFRACTION16chain C and (resseq 126:142)C126 - 142
17X-RAY DIFFRACTION17chain C and (resseq 143:170)C143 - 170
18X-RAY DIFFRACTION18chain C and (resseq 171:191)C171 - 191
19X-RAY DIFFRACTION19chain C and (resseq 192:215)C192 - 215
20X-RAY DIFFRACTION20chain D and (resseq 1:66)D1 - 66
21X-RAY DIFFRACTION21chain D and (resseq 67:191)D67 - 191
22X-RAY DIFFRACTION22chain D and (resseq 192:215)D192 - 215

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