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- PDB-5uun: Crystal structure of SARO_2595 from Novosphingobium aromaticivorans -

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Basic information

Entry
Database: PDB / ID: 5uun
TitleCrystal structure of SARO_2595 from Novosphingobium aromaticivorans
ComponentsGlutathione S-transferase-like protein
KeywordsTRANSFERASE / Bioenergy / GLBRC / lignin valorization
Function / homology
Function and homology information


transferase 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, 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 / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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
ACETATE ION / GLUTATHIONE / Glutathione S-transferase-like protein
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBingman, C.A. / Kontur, W.S. / Olmsted, C.N. / Fox, B.G. / Donohue, T.J.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Novosphingobium aromaticivoransuses a Nu-class glutathioneS-transferase as a glutathione lyase in breaking the beta-aryl ether bond of lignin.
Authors: Kontur, W.S. / Bingman, C.A. / Olmsted, C.N. / Wassarman, D.R. / Ulbrich, A. / Gall, D.L. / Smith, R.W. / Yusko, L.M. / Fox, B.G. / Noguera, D.R. / Coon, J.J. / Donohue, T.J.
History
DepositionFeb 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 4, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,50027
Polymers65,0312
Non-polymers2,46925
Water17,511972
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14040 Å2
ΔGint-79 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.590, 70.640, 168.570
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 Glutathione S-transferase-like protein


Mass: 32515.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199) (bacteria)
Strain: ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199
Gene: Saro_2595 / Cell line (production host): B834 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2G542
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 972 / 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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Saro protein at 277 mM was incubated with 10 mM reduced glutathione for 50 minutes prior to setting up crystallization experiments. An equal volume of protein solution and reservoir were ...Details: Saro protein at 277 mM was incubated with 10 mM reduced glutathione for 50 minutes prior to setting up crystallization experiments. An equal volume of protein solution and reservoir were deposited by a TTP Labtech Mosquito in a SD2 crystallization plate and allowed to equilibrate. The crystals were self-cryoprotected by the reservoir of 4 M ammonium acetate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2016
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.45→43.97 Å / Num. obs: 140421 / % possible obs: 96.48 % / Redundancy: 13.2 % / Biso Wilson estimate: 13.23 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04367 / Rpim(I) all: 0.01239 / Net I/σ(I): 36.36
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.2047 / Mean I/σ(I) obs: 8.82 / Num. unique obs: 11067 / CC1/2: 0.986 / Rpim(I) all: 0.06599 / % possible all: 76.88

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3c8e chain A

3c8e


Resolution: 1.45→43.975 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 11.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1357 1852 1.32 %Thin shells
Rwork0.1165 ---
obs0.1168 140406 96.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→43.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4502 0 164 972 5638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095003
X-RAY DIFFRACTIONf_angle_d1.3466779
X-RAY DIFFRACTIONf_dihedral_angle_d14.5351772
X-RAY DIFFRACTIONf_chiral_restr0.079676
X-RAY DIFFRACTIONf_plane_restr0.007918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48920.1541210.13748127X-RAY DIFFRACTION74
1.4892-1.5330.14611250.12399875X-RAY DIFFRACTION90
1.533-1.58250.12861360.11310525X-RAY DIFFRACTION96
1.5825-1.63910.12331570.108210786X-RAY DIFFRACTION98
1.6391-1.70470.12211380.109110798X-RAY DIFFRACTION99
1.7047-1.78230.11691340.112910843X-RAY DIFFRACTION99
1.7823-1.87630.12851680.113410845X-RAY DIFFRACTION99
1.8763-1.99380.14071290.116710941X-RAY DIFFRACTION99
1.9938-2.14780.12471310.112310986X-RAY DIFFRACTION99
2.1478-2.36390.12541870.107210965X-RAY DIFFRACTION100
2.3639-2.70590.13231080.113311124X-RAY DIFFRACTION100
2.7059-3.4090.15521930.122811156X-RAY DIFFRACTION100
3.409-43.99480.13491250.121311583X-RAY DIFFRACTION100

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