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- PDB-3c8e: Crystal Structure Analysis of yghU from E. Coli -

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Basic information

Entry
Database: PDB / ID: 3c8e
TitleCrystal Structure Analysis of yghU from E. Coli
ComponentsyghU, glutathione S-transferase homologue
KeywordsTRANSFERASE / glutathione transferase homologue / YghU / E. coli
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / disulfide oxidoreductase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-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 ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-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 / Disulfide-bond oxidoreductase YghU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsHarp, J. / Ladner, J.E. / Schaab, M.R. / Stourman, N.V. / Armstrong, R.N.
CitationJournal: Biochemistry / Year: 2011
Title: Structure and Function of YghU, a Nu-Class Glutathione Transferase Related to YfcG from Escherichia coli.
Authors: Stourman, N.V. / Branch, M.C. / Schaab, M.R. / Harp, J.M. / Ladner, J.E. / Armstrong, R.N.
History
DepositionFeb 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: yghU, glutathione S-transferase homologue
B: yghU, glutathione S-transferase homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0926
Polymers64,8632
Non-polymers1,2294
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.197, 73.455, 130.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein yghU, glutathione S-transferase homologue


Mass: 32431.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: yghU / Plasmid: pET-21b(+) plasmid (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold DE-3 (Stratagene) / References: UniProt: Q46845
#2: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


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


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 0.2M NaCl, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.00, 0.9795, 0.9790, 0.9500
DetectorType: MAR / Detector: CCD / Date: Jun 22, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
30.9791
40.951
ReflectionRedundancy: 6.6 % / Av σ(I) over netI: 9.4 / Number: 295858 / Rmerge(I) obs: 0.097 / Χ2: 1 / D res high: 1.89 Å / D res low: 50 Å / Num. obs: 44647 / % possible obs: 96.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.075099.810.0610.9947.7
3.234.0710010.0770.9257.6
2.823.2399.910.0880.9247.1
2.572.8299.610.1120.9656.8
2.382.5799.510.1391.0326.8
2.242.3898.810.1761.0586.7
2.132.249810.221.0536.6
2.042.1396.810.2711.0996.3
1.962.0494.810.3320.9625.7
1.891.9679.510.3920.9294.2
ReflectionResolution: 1.41→50 Å / Num. obs: 95609 / % possible obs: 87.7 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.109 / Χ2: 1.039 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.41-1.4630.65360870.72456.5
1.46-1.523.90.56779080.65473.4
1.52-1.594.70.51785960.74879.7
1.59-1.675.60.48891850.74185
1.67-1.787.60.52898370.78791
1.78-1.919.80.482103100.80295.1
1.91-2.1110.80.299105700.85797.3
2.11-2.4111.20.175107980.96198.7
2.41-3.0411.60.108109571.12599.5
3.04-5013.10.055113611.69399.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.274 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.197 8037 10 %RANDOM
Rwork0.162 ---
obs0.165 80150 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.609 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2---0.98 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4523 0 80 471 5074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224882
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.9536662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8645611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99723.852244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13315776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2921531
X-RAY DIFFRACTIONr_chiral_restr0.2470.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023873
X-RAY DIFFRACTIONr_nbd_refined0.220.22321
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23360
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2450
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.222
X-RAY DIFFRACTIONr_mcbond_it1.1911.52957
X-RAY DIFFRACTIONr_mcangle_it1.67724651
X-RAY DIFFRACTIONr_scbond_it2.61232221
X-RAY DIFFRACTIONr_scangle_it3.8264.51988
LS refinement shellResolution: 1.5→1.581 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.272 882 -
Rwork0.215 8027 -
all-8909 -
obs--100 %

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