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- PDB-8ix7: Functional significance of serine 13 in the active site of rice P... -

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Basic information

Entry
Database: PDB / ID: 8ix7
TitleFunctional significance of serine 13 in the active site of rice Phi-class glutathione S-transferase F3.
Componentsglutathione transferase
KeywordsPLANT PROTEIN / glutathion-S-transferase
Function / homology
Function and homology information


response to chemical / glutathione transferase / glutathione transferase activity
Similarity search - Function
Glutathione S-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / 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 transferase
Similarity search - Component
Biological speciesOryza sativa subsp. indica (long-grained rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsLee, W.C. / Kong, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1D1A1B07043467 Korea, Republic Of
CitationJournal: to be published
Title: Functional significance of serine 13 in the active site of rice Phi-class glutathione S-transferase F3.
Authors: Im, J.K. / Lee, W.C. / Kong, J. / Jo, H.J. / Kong, K.H.
History
DepositionMar 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glutathione transferase
B: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0754
Polymers49,4612
Non-polymers6152
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-25 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.960, 48.120, 80.340
Angle α, β, γ (deg.)90.000, 102.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein glutathione transferase / glutathione S-transferase F3


Mass: 24730.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. indica (long-grained rice)
Gene: Plk1 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2XC69
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.14 Å3/Da / Density % sol: 42.43 % / Mosaicity: 0.9 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.2M sodium acetate, 0.1M Tris HCl, 30 % (w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.7→78.484 Å / Num. all: 45629 / Num. obs: 45629 / % possible obs: 98.8 % / Redundancy: 3.6 % / Rpim(I) all: 0.045 / Rrim(I) all: 0.086 / Rsym value: 0.073 / Net I/av σ(I): 6.683 / Net I/σ(I): 10.5 / Num. measured all: 162265
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRsym value% possible all
1.7-1.792.80.3791.962360.2770.37993.5
1.79-1.93.60.2932.563010.1790.293100
1.9-2.033.70.1774.260030.1080.177100
2.03-2.193.70.1176.355410.0710.117100
2.19-2.43.70.0878.251580.0530.087100
2.4-2.693.70.06810.246420.0410.068100
2.69-3.13.70.05810.941160.0350.058100
3.1-3.83.70.0571034880.0340.057100
3.8-5.383.60.04511.827200.0280.04599.8
5.38-50.1623.40.05211.114240.0330.05292.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
DENZO3.3.20data reduction
MOLREPphasing
CNS1.3refinement
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BX9

1bx9


Resolution: 1.7→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2071 2313 5 %
Rwork0.181 43302 -
obs-45615 98.7 %
Solvent computationBsol: 49.9894 Å2
Displacement parametersBiso max: 67.96 Å2 / Biso mean: 21.9382 Å2 / Biso min: 8.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.967 Å20 Å2-4.455 Å2
2---1.7 Å2-0 Å2
3---2.668 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 40 421 3887
Biso mean--36.36 33.58 -
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.204
X-RAY DIFFRACTIONc_mcbond_it1.1831.5
X-RAY DIFFRACTIONc_scbond_it2.1962
X-RAY DIFFRACTIONc_mcangle_it1.7282
X-RAY DIFFRACTIONc_scangle_it3.3162.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.760.30461770.27533969414690.3
1.76-1.830.27982390.24424278451799.1
1.83-1.910.23092380.204843744612100
1.91-2.020.1922100.178543734583100
2.02-2.140.20742330.180243684601100
2.14-2.310.20732260.168943924618100
2.31-2.540.16772450.161143884633100
2.54-2.910.23042600.187343454605100
2.91-3.660.20022510.172944194670100
3.66-500.19282340.16944396463097.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top
X-RAY DIFFRACTION6GTT.parGTT.top

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