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- PDB-7y55: Crystal structure of a glutathione S-transferase Tau1 from Pinus ... -

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Basic information

Entry
Database: PDB / ID: 7y55
TitleCrystal structure of a glutathione S-transferase Tau1 from Pinus densata in complex with GSH
ComponentsPdGSTU1
KeywordsTRANSFERASE / Glutathione S-transferase / Tau calss / GSH
Function / homologyGlutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutaredoxin / Glutaredoxin / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta / GLUTATHIONE
Function and homology information
Biological speciesPinus densata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19113061058 Å
AuthorsQu, C. / Zeng, Q.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Syst Evol / Year: 2023
Title: Functional significance of asymmetrical retention of parental alleles in a hybrid pine species complex
Authors: Qu, C. / Kao, H.N. / Xu, H. / Wang, B.S. / Yang, Z.L. / Yang, Q. / Liu, G.F. / Wang, X.R. / Liu, Y.J. / Zeng, Q.Y.
History
DepositionJun 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.year / _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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PdGSTU1
B: PdGSTU1
C: PdGSTU1
D: PdGSTU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2328
Polymers110,0034
Non-polymers1,2294
Water2,504139
1
A: PdGSTU1
hetero molecules

C: PdGSTU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6164
Polymers55,0012
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_446-x-1/2,y-1/2,-z+11
Buried area3560 Å2
ΔGint-26 kcal/mol
Surface area19750 Å2
MethodPISA
2
B: PdGSTU1
hetero molecules

D: PdGSTU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6164
Polymers55,0012
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
Buried area3570 Å2
ΔGint-26 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.402, 55.509, 119.754
Angle α, β, γ (deg.)90.0, 112.498, 90.0
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 4 - 224 / Label seq-ID: 13 - 233

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22chain 'B'BB
33chain 'C'CC
44chain 'D'DD

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Components

#1: Protein
PdGSTU1


Mass: 27500.732 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: gene: PdSTU1 / Source: (gene. exp.) Pinus densata (plant) / Production host: Escherichia coli (E. coli) / References: glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE


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


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M MES monohydrate pH 5.5, 25% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 49207 / % possible obs: 94.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 37.8201064726 Å2 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.073 / Rrim(I) all: 0.182 / Χ2: 2.36 / Net I/σ(I): 3.3 / Num. measured all: 275021
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.19-2.233.30.70317170.7420.3890.8110.46866.6
2.23-2.273.60.68619140.7960.3670.7840.48774.4
2.27-2.313.80.66721230.8240.3490.7580.50281.1
2.31-2.3640.66522080.8220.3480.7560.586.7
2.36-2.414.30.623810.8630.3050.6770.53291.3
2.41-2.474.70.55524310.8990.2740.6220.52295.7
2.47-2.534.90.51725460.9240.2510.5770.53797.1
2.53-2.65.20.51625520.9250.2440.5730.57898.5
2.6-2.676.20.48125810.9470.2080.5250.57799.8
2.67-2.766.30.41725650.9680.1770.4540.56399.9
2.76-2.866.30.36126150.9710.1540.3930.60199.9
2.86-2.976.20.3125660.9550.1340.3380.689100
2.97-3.115.90.24426150.9820.1080.2670.78599.6
3.11-3.276.20.21325960.9820.0920.2330.88999.4
3.27-3.486.60.17325980.9910.0730.1881.088100
3.48-3.746.60.14725950.9860.0620.161.88899.9
3.74-4.126.20.11926040.9930.0520.132.16799.6
4.12-4.726.70.11326300.990.0470.1234.601100
4.72-5.946.40.10826520.990.0460.1184.93499.7
5.94-106.30.15127180.9680.0650.16516.23499.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
PHENIXphasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TOP

4top


Resolution: 2.19113061058→38.4344061754 Å / SU ML: 0.281497880785 / Cross valid method: NONE / σ(F): 1.34655140362 / Phase error: 39.1856010711
RfactorNum. reflection% reflection
Rfree0.302089815492 1994 4.07304518343 %
Rwork0.275615564752 46962 -
obs0.276769379248 48956 93.4792155964 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.5783773664 Å2
Refinement stepCycle: LAST / Resolution: 2.19113061058→38.4344061754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7291 0 80 139 7510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008224423084267567
X-RAY DIFFRACTIONf_angle_d1.2354155603810211
X-RAY DIFFRACTIONf_chiral_restr0.05124475888851047
X-RAY DIFFRACTIONf_plane_restr0.0062582955941313
X-RAY DIFFRACTIONf_dihedral_angle_d13.04188939142843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1912-2.24590.397037962425960.3702750264762270X-RAY DIFFRACTION63.7392241379
2.2459-2.30660.3699890353761170.3599701961592757X-RAY DIFFRACTION76.8038482095
2.3066-2.37450.3523153654541283022X-RAY DIFFRACTION85.9950859951
2.3745-2.45110.3830598803171410.348974018263322X-RAY DIFFRACTION93.016384636
2.4511-2.53870.3097729173671463446X-RAY DIFFRACTION96.7672413793
2.5387-2.64030.3563799258261510.3144842715943535X-RAY DIFFRACTION98.7674169346
2.6403-2.76050.3335711414161490.2955688125893529X-RAY DIFFRACTION99.7018162104
2.7605-2.9060.3236295851451530.2933671399183579X-RAY DIFFRACTION99.5731056564
2.906-3.0880.3110587505281510.2916120620933564X-RAY DIFFRACTION99.5444801715
3.088-3.32630.2695290395761513559X-RAY DIFFRACTION99.2509363296
3.3263-3.66080.2986859582281510.2614620801843583X-RAY DIFFRACTION99.5467875233
3.6608-4.18990.2671917761551510.2451869200543579X-RAY DIFFRACTION99.4136460554
4.1899-5.27670.2560019055291540.2322340276473615X-RAY DIFFRACTION99.4721562418
5.2767-100.3118128825651550.2633050149633602X-RAY DIFFRACTION96.7301750772

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