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- PDB-6o2e: GCN4 with asparagine at position 18 -

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Basic information

Entry
Database: PDB / ID: 6o2e
TitleGCN4 with asparagine at position 18
ComponentsGeneral control protein GCN4
KeywordsTRANSCRIPTION / GCN4 / PEG / PEGylation
Function / homology
Function and homology information


protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain
Similarity search - Domain/homology
General control transcription factor GCN4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.896 Å
AuthorsDraper, S.R.E. / Xiao, Q. / Smith, M. / Price, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R15 United States
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Influence of PEGylation on the Strength of Protein Surface Salt Bridges.
Authors: Xiao, Q. / Draper, S.R.E. / Smith, M.S. / Brown, N. / Pugmire, N.A.B. / Ashton, D.S. / Carter, A.J. / Lawrence, E.E.K. / Price, J.L.
History
DepositionFeb 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)3,7211
Polymers3,7211
Non-polymers00
Water75742
1
A: General control protein GCN4

A: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)7,4432
Polymers7,4432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area1940 Å2
ΔGint-21 kcal/mol
Surface area5110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)19.251, 30.016, 107.053
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-140-

HOH

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Components

#1: Protein/peptide General control protein GCN4 / Amino acid biosynthesis regulatory protein


Mass: 3721.350 Da / Num. of mol.: 1 / Mutation: H266N / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P03069
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Pact premier C1

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5406 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.896→53.526 Å / Num. obs: 4721

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing
RefinementResolution: 1.896→53.526 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.35
RfactorNum. reflection% reflection
Rfree0.2474 472 10 %
Rwork0.2144 --
obs0.2179 4721 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.99 Å2 / Biso mean: 26.4734 Å2 / Biso min: 8.17 Å2
Refinement stepCycle: final / Resolution: 1.896→53.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms260 0 0 42 302
Biso mean---37.13 -
Num. residues----31
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8961-2.17050.28581510.23921398154998
2.1705-2.73450.27761610.222614371598100
2.7345-53.54780.22171600.20261414157499

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