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- PDB-3rbt: Crystal structure of glutathione S-transferase Omega 3 from the s... -

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Basic information

Entry
Database: PDB / ID: 3rbt
TitleCrystal structure of glutathione S-transferase Omega 3 from the silkworm Bombyx mori
ComponentsGlutathione transferase o1
KeywordsTRANSFERASE / glutathione S-transferase Omega3
Function / homology
Function and homology information


glutathione transferase activity / oxidoreductase activity / cytoplasm
Similarity search - Function
Glutathione S-transferase, omega-class / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / 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, omega-class / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / 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 transferase o1
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, B.-Y. / Ma, X.-X. / Tan, X. / Yang, J.-P. / Zhang, N.-N. / Li, W.-F. / Chen, Y. / Xia, Q. / Zhou, C.-Z.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure-guided activity restoration of the silkworm glutathione transferase Omega GSTO3-3
Authors: Chen, B.-Y. / Ma, X.-X. / Guo, P.-C. / Tan, X. / Li, W.-F. / Yang, J.-P. / Zhang, N.-N. / Chen, Y. / Xia, Q. / Zhou, C.-Z.
History
DepositionMar 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references / Derived calculations
Revision 1.2Nov 1, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 transferase o1
B: Glutathione transferase o1
C: Glutathione transferase o1
D: Glutathione transferase o1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,9878
Polymers117,6184
Non-polymers3684
Water6,431357
1
A: Glutathione transferase o1
hetero molecules

A: Glutathione transferase o1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9934
Polymers58,8092
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2
B: Glutathione transferase o1
hetero molecules

C: Glutathione transferase o1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9934
Polymers58,8092
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_445x-1/2,-y-1/2,-z1
3
C: Glutathione transferase o1
hetero molecules

B: Glutathione transferase o1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9934
Polymers58,8092
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_545x+1/2,-y-1/2,-z1
4
D: Glutathione transferase o1
hetero molecules

D: Glutathione transferase o1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9934
Polymers58,8092
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Unit cell
Length a, b, c (Å)108.537, 139.030, 128.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23A

NCS domain segments:

Component-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERBB6 - 24012 - 246
21VALVALAA11 - 24017 - 246
12SERSERCC6 - 24012 - 246
22VALVALAA11 - 24017 - 246
13HISHISDD-1 - 2405 - 246
23VALVALAA11 - 24017 - 246

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Glutathione transferase o1 / glutathione S-transferase Omega 3


Mass: 29404.561 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q1HPV9, glutathione transferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M magnesium chloride, 0.1M Tris-HCl pH 8.5, 25% polyethylene glycol 3350, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 49572 / % possible obs: 99.8 %
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EEM

1eem


Resolution: 2.2→41.5 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.902 / SU B: 14.251 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26288 2509 5.1 %RANDOM
Rwork0.21503 ---
obs0.21748 47061 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.236 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2---0.68 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7857 0 24 357 8238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228106
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.96110976
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0815926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6323.093430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.161151396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0711568
X-RAY DIFFRACTIONr_chiral_restr0.0710.21134
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216289
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4031.54673
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.77827587
X-RAY DIFFRACTIONr_scbond_it1.22933433
X-RAY DIFFRACTIONr_scangle_it2.0714.53389
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B1920LOOSE POSITIONAL0.45
1B1920LOOSE THERMAL1.4210
2C1892LOOSE POSITIONAL1.375
2C1892LOOSE THERMAL1.6810
3D1942LOOSE POSITIONAL0.455
3D1942LOOSE THERMAL1.0310
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 176 -
Rwork0.216 3405 -
obs--98.27 %
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)
11.8265-0.1311-0.09421.88580.03031.78-0.02090.10110.1246-0.17460.02060.12880.0088-0.0460.00030.0684-0.0476-0.01560.0776-0.0070.0628-11.841-17.66323.102
21.25930.2931-0.6171.4420.17622.77210.03850.01520.13370.0214-0.0691-0.1265-0.09420.11250.03050.05070.0093-0.02950.11910.06170.0843-40.562-17.9239.736
32.5320.41580.31652.1839-0.3282.99270.1294-0.0029-0.26810.1206-0.0830.09880.1809-0.2007-0.04630.06640.01850.01290.12-0.03790.0783-11.397-51.8626.583
41.7438-0.17370.34271.70440.12022.3517-0.05080.0989-0.2078-0.15530.0529-0.26850.10350.1257-0.00210.0722-0.04260.07030.0802-0.00680.1503-40.247-52.51525.327
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 240
2X-RAY DIFFRACTION2B6 - 240
3X-RAY DIFFRACTION3C6 - 240
4X-RAY DIFFRACTION4D-1 - 240

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