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- PDB-3d0z: Structural charcaterization of an engineered allosteric protein -

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Basic information

Entry
Database: PDB / ID: 3d0z
TitleStructural charcaterization of an engineered allosteric protein
ComponentsGlutathione S-transferase class-mu 26 kDa isozyme
KeywordsTRANSFERASE / protein design / engineered allostery / pH-switch
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
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 / 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, 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
GLUTATHIONE / Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSagermann, M.
CitationJournal: Protein Sci. / Year: 2009
Title: Using affinity chromatography to engineer and characterize pH-dependent protein switches.
Authors: Sagermann, M. / Chapleau, R.R. / DeLorimier, E. / Lei, M.
History
DepositionMay 2, 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 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase class-mu 26 kDa isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4052
Polymers25,0981
Non-polymers3071
Water1,910106
1
A: Glutathione S-transferase class-mu 26 kDa isozyme
hetero molecules

A: Glutathione S-transferase class-mu 26 kDa isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8114
Polymers50,1962
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4210 Å2
ΔGint-22 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.500, 93.500, 58.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThis molecule is a homodimer under physiological conditions. In the crystal the monomers are related by a crystallographic 2-fold axis.

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Components

#1: Protein Glutathione S-transferase class-mu 26 kDa isozyme / GST 26 / Sj26 antigen / SjGST


Mass: 25098.152 Da / Num. of mol.: 1 / Mutation: L50H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / References: UniProt: P08515, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG8000, 50mM TRIS, 5mM B-mercaptoethanol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97984 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 19, 2008 / Details: mirrors
RadiationMonochromator: SI crystal focused / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97984 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 17056 / Num. obs: 16796 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.28 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.36
Reflection shellResolution: 2.5→2.7 Å / Redundancy: 3.86 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 6.92 / Num. unique all: 3367 / % possible all: 96.1

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Processing

Software
NameClassification
XDSdata scaling
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBid: 1GNE (residues 1-214)

1gne


Resolution: 2.5→20 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Details: The c-terminal residues HPPK could not be modeled into the density reliably.
RfactorNum. reflection% reflectionSelection details
Rfree0.311 1278 -random
Rwork0.239 ---
all-16441 --
obs-16403 99.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.556 Å20 Å20 Å2
2---4.556 Å20 Å2
3---9.113 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 20 106 1889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0078
X-RAY DIFFRACTIONc_angle_deg1.4

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