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- PDB-3vpq: Crystal structure of Bombyx mori sigma-class glutathione transfer... -

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Basic information

Entry
Database: PDB / ID: 3vpq
TitleCrystal structure of Bombyx mori sigma-class glutathione transferase in complex with glutathione
ComponentsGlutathione S-transferase sigma
KeywordsTRANSFERASE / alpha/beta-barrel / glutathione
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-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 / Glutathione S-transferase, N-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 / DI(HYDROXYETHYL)ETHER / S-1,2-PROPANEDIOL / glutathione transferase
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsYamamoto, K. / Higashiura, A. / Nakagawa, A. / Suzuki, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Crystal structure of a Bombyx mori sigma-class glutathione transferase exhibiting prostaglandin E synthase activity
Authors: Yamamoto, K. / Higashiura, A. / Suzuki, M. / Aritake, K. / Urade, Y. / Uodome, N. / Nakagawa, A.
History
DepositionMar 8, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 8, 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_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 sigma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,78214
Polymers23,3701
Non-polymers1,41313
Water1,24369
1
A: Glutathione S-transferase sigma
hetero molecules

A: Glutathione S-transferase sigma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,56528
Polymers46,7392
Non-polymers2,82526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.081, 56.081, 209.244
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutathione S-transferase sigma


Mass: 23369.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: GST sigma / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CCJ4, glutathione transferase

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Non-polymers , 5 types, 82 molecules

#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, pH7.5, containing 30% PEG 400, 20% 1,2-propanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→35.592 Å / Num. obs: 22392 / % possible obs: 99.8 % / Observed criterion σ(I): 3
Reflection shellHighest resolution: 1.7 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VPT

3vpt


Resolution: 1.702→31.7 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 20.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 1133 5.08 %
Rwork0.1877 --
obs0.1896 22290 99.46 %
Solvent computationShrinkage radii: 0.29 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.342 Å2 / ksol: 0.439 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8538 Å2-0 Å2-0 Å2
2--1.8538 Å20 Å2
3----3.7077 Å2
Refinement stepCycle: LAST / Resolution: 1.702→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 0 93 69 1805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161784
X-RAY DIFFRACTIONf_angle_d1.5332387
X-RAY DIFFRACTIONf_dihedral_angle_d20.455669
X-RAY DIFFRACTIONf_chiral_restr0.098249
X-RAY DIFFRACTIONf_plane_restr0.009306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7021-1.77960.28811150.26212500X-RAY DIFFRACTION97
1.7796-1.87340.30041550.23242596X-RAY DIFFRACTION100
1.8734-1.99080.23991390.21052579X-RAY DIFFRACTION100
1.9908-2.14450.20431420.18542610X-RAY DIFFRACTION100
2.1445-2.36020.22231540.1732616X-RAY DIFFRACTION100
2.3602-2.70170.18561470.17022651X-RAY DIFFRACTION100
2.7017-3.40340.21891430.16182693X-RAY DIFFRACTION100
3.4034-35.60010.24031380.19692912X-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)
11.3929-0.2411-0.2351.5901-0.06332.6887-0.1882-0.0625-0.3211-0.0764-0.0259-0.33861.3452-0.09470.13040.6335-0.01650.06630.1688-0.03080.273420.069-33.715214.2936
24.74731.1473-0.04314.09530.16182.7649-0.0259-0.1587-0.1649-0.42840.1201-0.0460.4325-0.69110.00880.3044-0.07650.00710.2782-0.01070.215712.9921-28.720125.9098
31.9409-0.1630.10591.73561.10480.7317-0.0285-0.1456-0.10760.1426-0.1542-0.01440.78360.54970.10860.43590.20380.0460.30630.0740.252530.2516-28.987917.9146
42.6231-0.3991-0.43481.3111-0.02412.60990.0409-0.1170.1392-0.1497-0.01740.08080.2120.16690.05110.24410.0280.0070.25920.00330.30126.8042-13.872810.5785
53.3588-1.8278-0.49212.6370.75144.99330.0244-0.0136-0.0177-0.0044-0.36320.3884-0.6159-1.59890.33710.32030.0909-0.06810.6188-0.03240.55247.0449-5.02249.9834
63.7638-2.5074-2.07623.62711.69422.44940.2853-0.2051-0.1691-0.3727-0.170.1168-0.41320.1204-0.05890.3375-0.0197-0.02910.23730.02150.264824.3535-8.3410.665
71.77650.9155-0.49821.0832-0.43283.0118-0.04090.16850.3625-0.15360.0030.07120.5966-0.01790.00770.3310.04040.00450.2275-0.00360.276624.5172-20.49744.0611
82.6131-0.8216-1.45442.91151.29823.283-0.1631-0.1221-0.04690.0637-0.18251.2639-0.1812-0.82470.11560.57850.0014-0.31350.54320.01030.632114.0252-13.2561-3.7866
91.0669-1.82731.46593.1304-2.51872.02860.26030.0722-0.1167-1.0586-0.29540.56450.8948-0.21510.00020.51830.01-0.00570.25060.00390.323723.3116-22.7767-3.3174
101.9442-1.0144-1.33991.59551.35981.334-0.17920.1552-0.1954-0.3375-0.12560.05540.8482-0.14110.56290.82570.00960.10450.2543-0.11590.334518.1545-33.73412.7933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:35)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 36:52)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 53:81)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 82:106)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 107:124)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 125:139)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 140:167)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 168:176)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 177:187)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 188:204)

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