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- PDB-1k0c: Ure2p in complex with S-p-nitrobenzylglutathione -

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Basic information

Entry
Database: PDB / ID: 1k0c
TitleUre2p in complex with S-p-nitrobenzylglutathione
ComponentsURE2 PROTEIN
KeywordsGENE REGULATION / Nitrate assimilation / Structural genomics
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
GLUTATHIONE / S-(P-NITROBENZYL)GLUTATHIONE / 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. / Melki, R. / Morera, S.
Citation
Journal: Biochemistry / Year: 2001
Title: Crystal structures of the yeast prion Ure2p functional region in complex with glutathione and related compounds.
Authors: Bousset, L. / Belrhali, H. / Melki, R. / Morera, S.
#1: 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.
History
DepositionSep 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2011Group: Non-polymer description
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: URE2 PROTEIN
B: URE2 PROTEIN
C: URE2 PROTEIN
D: URE2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9748
Polymers119,3404
Non-polymers1,6354
Water2,900161
1
A: URE2 PROTEIN
B: URE2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5554
Polymers59,6702
Non-polymers8852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-33 kcal/mol
Surface area19780 Å2
MethodPISA
2
C: URE2 PROTEIN
D: URE2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4204
Polymers59,6702
Non-polymers7502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-33 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.736, 123.214, 168.182
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


Mass: 29834.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P23202
#2: Chemical ChemComp-GTB / S-(P-NITROBENZYL)GLUTATHIONE


Mass: 442.444 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H22N4O8S
#3: Chemical ChemComp-GSH / GLUTATHIONE


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


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: peg 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Bousset, L., (2001) Structure, 9, 39.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
230 %PEG10001reservoir
3160 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: Sep 4, 2000
RadiationProtocol: 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: 40155 / Num. obs: 38381 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rsym value: 0.08 / Net I/σ(I): 7.4
Reflection shellResolution: 2.5→2.6 Å / % possible all: 93.5
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 94 % / Num. measured all: 390942 / Rmerge(I) obs: 0.08

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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 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.267 1857 RANDOM
Rwork0.214 --
all-40155 -
obs-37263 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.625 Å20 Å20 Å2
2---3.845 Å20 Å2
3----5.78 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7628 0 110 161 7899
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_mcbond_it1.2881.5
X-RAY DIFFRACTIONc_scbond_it1.9962
X-RAY DIFFRACTIONc_mcangle_it2.1582
X-RAY DIFFRACTIONc_scangle_it2.9752.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4gtt_xplor.param
X-RAY DIFFRACTION5gtb_xplor.param
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5

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