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- PDB-6t2t: Crystal structure of Drosophila melanogaster glutathione S-transf... -

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Basic information

Entry
Database: PDB / ID: 6t2t
TitleCrystal structure of Drosophila melanogaster glutathione S-transferase epsilon 14 in complex with glutathione and 2-methyl-2,4-pentanediol
ComponentsGlutathione S-transferase E14
KeywordsTRANSFERASE / glutathione transferase / steroid isomerase
Function / homology
Function and homology information


ecdysteroid biosynthetic process / steroid delta-isomerase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cholesterol homeostasis / response to toxic substance / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
GLUTATHIONE / Glutathione S-transferase E14
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsSkerlova, J. / Lindstrom, H. / Sjodin, B. / Gonis, E. / Neiers, F. / Mannervik, B. / Stenmark, P.
Funding support Czech Republic, Sweden, 3items
OrganizationGrant numberCountry
Ministry of Education (Czech Republic)CZ.02.2.69/0.0/0.0/16_027/0008477 Czech Republic
Swedish Research Council2015-04222 Sweden
Swedish Research Council2018-03406 Sweden
CitationJournal: Febs Lett. / Year: 2020
Title: Structure and steroid isomerase activity of Drosophila glutathione transferase E14 essential for ecdysteroid biosynthesis.
Authors: Skerlova, J. / Lindstrom, H. / Gonis, E. / Sjodin, B. / Neiers, F. / Stenmark, P. / Mannervik, B.
History
DepositionOct 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase E14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9053
Polymers27,4791
Non-polymers4252
Water4,270237
1
A: Glutathione S-transferase E14
hetero molecules

A: Glutathione S-transferase E14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8106
Polymers54,9592
Non-polymers8514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5160 Å2
ΔGint-57 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.201, 76.201, 100.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

21A-550-

HOH

31A-605-

HOH

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Components

#1: Protein Glutathione S-transferase E14 / Protein noppera-bo


Mass: 27479.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GstE14, GSTD14-14, nobo, CG4688 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7JYX0, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.73 % / Description: cubic
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M MOPS/HEPES pH 7.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, and 12.5% v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→53.88 Å / Num. obs: 73240 / % possible obs: 99.8 % / Redundancy: 22.4 % / CC1/2: 1 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.019 / Rrim(I) all: 0.094 / Net I/σ(I): 18.2 / Num. measured all: 1637590 / Scaling rejects: 58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.3-1.328.40.8732871034240.7640.3110.9292.196.7
7.12-53.8821.30.0321186255610.0070.03357.199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
Aimless0.7.2data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vwx

3vwx


Resolution: 1.3→50.38 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.589 / SU ML: 0.025 / SU R Cruickshank DPI: 0.0406 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.039
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1636 3596 4.9 %RANDOM
Rwork0.1567 ---
obs0.1571 69566 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.46 Å2 / Biso mean: 13.087 Å2 / Biso min: 6.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.35 Å2
Refinement stepCycle: final / Resolution: 1.3→50.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 28 238 2114
Biso mean--11.77 25.37 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132133
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171967
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.6382921
X-RAY DIFFRACTIONr_angle_other_deg1.6011.5724590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0485276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76922.222117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25515376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1271514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022480
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02466
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 250 -
Rwork0.236 4914 -
all-5164 -
obs--96.87 %

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