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- PDB-3ibh: Crystal structure of Saccharomyces cerevisiae Gtt2 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3ibh
TitleCrystal structure of Saccharomyces cerevisiae Gtt2 in complex with glutathione
ComponentsSaccharomyces cerevisiae Gtt2
KeywordsTRANSFERASE / glutathione S-transferase
Function / homology
Function and homology information


glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / glutathione binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / mitochondrion / cytoplasm
Similarity search - Function
Gtt2-like, C-terminal / Gtt2-like, N-terminal / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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. ...Gtt2-like, C-terminal / Gtt2-like, N-terminal / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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
GLUTATHIONE / Glutathione S-transferase 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMa, X.X. / Jiang, Y.L. / He, Y.X. / Bao, R. / Chen, Y.X. / Zhou, C.Z.
CitationJournal: Embo Rep. / Year: 2009
Title: Structures of yeast glutathione-S-transferase Gtt2 reveal a new catalytic type of GST family.
Authors: Ma, X.X. / Jiang, Y.L. / He, Y.X. / Bao, R. / Chen, Y.X. / Zhou, C.Z.
History
DepositionJul 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 7, 2011Group: Non-polymer description
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Saccharomyces cerevisiae Gtt2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6842
Polymers26,3771
Non-polymers3071
Water2,090116
1
A: Saccharomyces cerevisiae Gtt2
hetero molecules

A: Saccharomyces cerevisiae Gtt2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3684
Polymers52,7532
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4940 Å2
ΔGint-32 kcal/mol
Surface area17510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.774, 88.774, 69.102
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Saccharomyces cerevisiae Gtt2 / GST-II


Mass: 26376.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: GTT2, L0560, YLL060C / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q12390, 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.: 116 / 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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, 2M ammoniun sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 18606 / Num. obs: 17631 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 15.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 5.9 / Num. unique all: 1778 / Rsym value: 0.245 / % possible all: 96.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ERG

3erg


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.144 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 950 5.1 %RANDOM
Rwork0.20811 ---
obs0.21002 17631 99.26 %-
all-18606 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.487 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å2-0.75 Å20 Å2
2---1.51 Å20 Å2
3---2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1653 0 20 116 1789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221711
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9882319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.325207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51123.61172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4251511
X-RAY DIFFRACTIONr_chiral_restr0.0940.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211279
X-RAY DIFFRACTIONr_mcbond_it0.6791.51039
X-RAY DIFFRACTIONr_mcangle_it1.2621682
X-RAY DIFFRACTIONr_scbond_it1.9383672
X-RAY DIFFRACTIONr_scangle_it3.1234.5637
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 81 -
Rwork0.265 1221 -
obs--96.02 %

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