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- PDB-2ycd: Structure of a novel Glutathione Transferase from Agrobacterium t... -

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Basic information

Entry
Database: PDB / ID: 2ycd
TitleStructure of a novel Glutathione Transferase from Agrobacterium tumefaciens.
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / SOIL BACTERIA / HERBICIDE DETOXIFICATION
Function / homology
Function and homology information


Glutathione S-transferase, C-terminal domain / 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...Glutathione S-transferase, C-terminal domain / 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-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
S-(P-NITROBENZYL)GLUTATHIONE / PHOSPHATE ION / Glutathione S-transferase
Similarity search - Component
Biological speciesAGROBACTERIUM TUMEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsSkopelitou, K. / Dhavala, P. / Papageorgiou, A.C. / Labrou, N.E.
CitationJournal: Plos One / Year: 2012
Title: A Glutathione Transferase from Agrobacterium Tumefaciens Reveals a Novel Class of Bacterial Gst Superfamily.
Authors: Skopelitou, K. / Dhavala, P. / Papageorgiou, A.C. / Labrou, N.E.
History
DepositionMar 13, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Other
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7103
Polymers26,1731
Non-polymers5372
Water5,639313
1
A: GLUTATHIONE S-TRANSFERASE
hetero molecules

A: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4216
Polymers52,3462
Non-polymers1,0754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5430 Å2
ΔGint-21.7 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.200, 95.500, 88.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2023-

HOH

21A-2047-

HOH

31A-2166-

HOH

41A-2184-

HOH

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE


Mass: 26172.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AGROBACTERIUM TUMEFACIENS (bacteria) / Strain: C53 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CFJ9
#2: Chemical ChemComp-GTB / S-(P-NITROBENZYL)GLUTATHIONE


Mass: 442.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N4O8S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.3 Å3/Da / Density % sol: 46.5 % / Description: NONE
Crystal growpH: 8.3 / Details: 1.4 M NA/K PHOSPHATE, PH 8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 41008 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.9
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.1 / % possible all: 99.9

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
SHELXphasing
SHARPphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.4→19.766 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 16.75 / Stereochemistry target values: ML
Details: FIRST 13 RESIDUES FROM THE N-TERMINAL WERE NOT MODELLED OWING TO HIGH FLEXIBILITY.
RfactorNum. reflection% reflection
Rfree0.1865 2089 5.1 %
Rwork0.1725 --
obs0.1732 41008 99.48 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.862 Å2 / ksol: 0.422 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7233 Å20 Å20 Å2
2--0.7228 Å20 Å2
3----2.4461 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 35 313 2051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081844
X-RAY DIFFRACTIONf_angle_d1.1472512
X-RAY DIFFRACTIONf_dihedral_angle_d15.341707
X-RAY DIFFRACTIONf_chiral_restr0.076268
X-RAY DIFFRACTIONf_plane_restr0.006329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.43260.24621440.23092557X-RAY DIFFRACTION100
1.4326-1.46840.21431530.21582582X-RAY DIFFRACTION100
1.4684-1.50810.20551240.19482571X-RAY DIFFRACTION100
1.5081-1.55250.24741440.18862578X-RAY DIFFRACTION100
1.5525-1.60250.2141310.18742588X-RAY DIFFRACTION100
1.6025-1.65980.24511270.17862604X-RAY DIFFRACTION100
1.6598-1.72620.21051280.17582593X-RAY DIFFRACTION100
1.7262-1.80470.16371340.17522609X-RAY DIFFRACTION100
1.8047-1.89980.19451570.17112552X-RAY DIFFRACTION100
1.8998-2.01870.18741540.16882589X-RAY DIFFRACTION100
2.0187-2.17440.18421380.172617X-RAY DIFFRACTION100
2.1744-2.39290.16331470.16192613X-RAY DIFFRACTION100
2.3929-2.73840.1671340.16292634X-RAY DIFFRACTION100
2.7384-3.44710.20871380.15782643X-RAY DIFFRACTION100
3.4471-19.76820.15561360.17532589X-RAY DIFFRACTION93

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