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- PDB-1hqo: CRYSTAL STRUCTURE OF THE NITROGEN REGULATION FRAGMENT OF THE YEAS... -

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Basic information

Entry
Database: PDB / ID: 1hqo
TitleCRYSTAL STRUCTURE OF THE NITROGEN REGULATION FRAGMENT OF THE YEAST PRION PROTEIN URE2P
ComponentsURE2 PROTEIN
KeywordsSIGNALING PROTEIN / glutathione S-transferase superfamily fold
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 / MAD / Resolution: 2.3 Å
AuthorsUmland, T.C. / Taylor, K.L. / Rhee, S. / Wickner, R.B. / Davies, D.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: The crystal structure of the nitrogen regulation fragment of the yeast prion protein Ure2p.
Authors: Umland, T.C. / Taylor, K.L. / Rhee, S. / Wickner, R.B. / Davies, D.R.
History
DepositionDec 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: URE2 PROTEIN
B: URE2 PROTEIN


Theoretical massNumber of molelcules
Total (without water)59,8762
Polymers59,8762
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-22 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.310, 69.190, 149.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer. The dimer was contained within the asymmetric unit.

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Components

#1: Protein URE2 PROTEIN


Mass: 29937.945 Da / Num. of mol.: 2 / Fragment: NITROGEN REGULATION FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: URE2 / Plasmid: PFLAG / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: P23202
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.84 %
Description: The model was refined against the remote data set (0.9686 A).
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.8
Details: NaCl, Bicine, Tris-HCl, alpha-chymotrypsin, pH 8.8, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.25 mg/mlprotein1drop
220 mMTris-HCl1drop
30.3 M1dropNaCl
40.01-0.001 mg/mlalpha-chymotrypsin1drop
52.5-3.0 M1reservoirNaCl
6100 mMBicine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9791, 0.9789, 0.9686
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 2, 2000
RadiationMonochromator: Si monochomator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97891
30.96861
ReflectionResolution: 2.3→20 Å / Num. all: 29499 / Num. obs: 168715 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 50.9 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.4
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.32 / Num. unique all: 2941 / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 29499 / Num. measured all: 168715
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.32

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Processing

Software
NameVersionClassification
SOLVEphasing
SnBAND PHASES-95phasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESV. 95phasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1343 5 %random
Rwork0.221 ---
all-30417 --
obs-27024 88.8 %-
Displacement parametersBiso mean: 55.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 0 204 3868
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.63
X-RAY DIFFRACTIONc_bond_d0.0118
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it2.11.5
X-RAY DIFFRACTIONc_mcangle_it3.42
X-RAY DIFFRACTIONc_scbond_it32
X-RAY DIFFRACTIONc_scangle_it4.22.5
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.358 108 -
Rwork0.315 2070 -
obs-2070 69.6 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 55.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
X-RAY DIFFRACTIONc_mcbond_it2.11.5
X-RAY DIFFRACTIONc_scbond_it32
X-RAY DIFFRACTIONc_mcangle_it3.42
X-RAY DIFFRACTIONc_scangle_it4.22.5
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.358 / Rfactor Rwork: 0.315

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