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- PDB-6m1t: Bacterial beta class Sphingomonas chungbukensis Glutathione S-tra... -

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Basic information

Entry
Database: PDB / ID: 6m1t
TitleBacterial beta class Sphingomonas chungbukensis Glutathione S-transferase
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / detoxification / GSH
Function / homology
Function and homology information


glutathione metabolic process / transferase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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 ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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
CYSTEINE / GLUTATHIONE / Glutathione S-transferase
Similarity search - Component
Biological speciesSphingobium chungbukense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsHan, Y.H. / Chung, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Korea)2018R1A6A3A11051079 Korea, Republic Of
CitationJournal: To Be Published
Title: Bacterial beta class Sphingomonas chungbukensis Glutathione S-transferase
Authors: Han, Y.H. / Chung, Y.J.
History
DepositionFeb 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1709
Polymers42,8832
Non-polymers1,2877
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-46 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.634, 95.447, 99.567
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutathione S-transferase


Mass: 21441.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium chungbukense (bacteria) / Gene: phnC, YP76_23560 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O30347

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Non-polymers , 5 types, 121 molecules

#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 50% saturated ammonium sulfate, 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 40525 / % possible obs: 99.3 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.053 / Χ2: 3.344 / Net I/σ(I): 31.6 / Num. measured all: 276554
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.8370.15420331.5541100
1.83-1.867.20.14219701.7011100
1.86-1.97.10.11920261.7921100
1.9-1.947.10.11420101.981100
1.94-1.987.10.10220282.161100
1.98-2.037.10.09619802.2611100
2.03-2.087.10.08520272.5841100
2.08-2.1370.07819952.705199.9
2.13-2.270.07520372.9161100
2.2-2.2770.0720152.9951100
2.27-2.356.90.06420033.095199.9
2.35-2.446.90.06120393.323199.6
2.44-2.556.80.05820153.532199.6
2.55-2.696.80.05620413.757199.4
2.69-2.866.70.05420283.922199.4
2.86-3.086.70.04920234.379198.9
3.08-3.396.70.04820325.417199
3.39-3.886.50.04420395.855198
3.88-4.886.10.0420785.826198.3
4.88-505.70.03921066.544193.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å43.04 Å
Translation2.2 Å43.04 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.8.3phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F2E

1f2e


Resolution: 1.9→43.07 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.347 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1622 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.154
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 1769 5.1 %RANDOM
Rwork0.2112 ---
obs0.2134 33012 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77 Å2 / Biso mean: 22.381 Å2 / Biso min: 8.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.9→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 78 114 3180
Biso mean--29.3 27.32 -
Num. residues----402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133130
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172946
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.644248
X-RAY DIFFRACTIONr_angle_other_deg1.7331.5836827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8185400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32421.908131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50915476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0051514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023498
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02620
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 118 -
Rwork0.227 2419 -
all-2537 -
obs--100 %

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