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- PDB-1g6w: CRYSTAL STRUCTURE OF THE GLOBULAR REGION OF THE PRION PROTEIN URE... -

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Basic information

Entry
Database: PDB / ID: 1g6w
TitleCRYSTAL STRUCTURE OF THE GLOBULAR REGION OF THE PRION PROTEIN URE2 FROM THE YEAST SACCAROMYCES CEREVISIAE
ComponentsURE2 PROTEIN
KeywordsSTRUCTURAL GENOMICS / GST SUPERFAMILY
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / protein urmylation / glutathione peroxidase / : / regulation of nitrogen utilization / glutathione peroxidase activity / glutathione transferase activity / nitrate assimilation / phosphoprotein binding / transcription corepressor activity / cytoplasm
Similarity search - Function
Transcriptional regulator Ure2 / 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. ...Transcriptional regulator Ure2 / 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
Transcriptional regulator URE2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBousset, L. / Belrhali, H. / Janin, J. / Melki, R. / Morera, S.
Citation
Journal: Structure / Year: 2001
Title: Structure of the globular region of the prion protein Ure2 from the yeast Saccharomyces cerevisiae.
Authors: Bousset, L. / Belrhali, H. / Janin, J. / Melki, R. / Morera, S.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Structural Characterization of Saccharomyces cerevisiae Prion-like Protein Ure2
Authors: Thual, C. / Komar, A.A. / Bousset, L. / Fernandez-Bellot, E. / Cullin, C. / Melki, R.
History
DepositionNov 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: URE2 PROTEIN
B: URE2 PROTEIN
C: URE2 PROTEIN
D: URE2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)119,8644
Polymers119,8644
Non-polymers00
Water5,152286
1
A: URE2 PROTEIN
B: URE2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)59,9322
Polymers59,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-25 kcal/mol
Surface area20970 Å2
MethodPISA
2
C: URE2 PROTEIN
D: URE2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)59,9322
Polymers59,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-24 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.680, 125.020, 159.950
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
URE2 PROTEIN / URE2P


Mass: 29966.104 Da / Num. of mol.: 4 / Fragment: GLOBULAR DOMAIN (RESIDUES 94-354)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: URE2 OR YNL229C OR N1165 / Plasmid: PET3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P23202
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, CaCl2 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
228 %PEG40001reservoir
3260 mM1reservoirCaCl2
4100 mMTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 1999
RadiationMonochromator: Asymmetric Laue C111 Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 37704 / Num. obs: 36861 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 44.454 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 5.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.291 / % possible all: 95
Reflection
*PLUS
Num. measured all: 277255
Reflection shell
*PLUS
% possible obs: 95 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2696 1842 RANDOM
Rwork0.21 --
all0.252 37704 -
obs0.24 36861 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8057 0 0 286 8343
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006457
X-RAY DIFFRACTIONc_angle_deg1.24835
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.41 Å2

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