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- PDB-4nj0: GCN4-p1 single Val9 to Ile mutant -

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Basic information

Entry
Database: PDB / ID: 4nj0
TitleGCN4-p1 single Val9 to Ile mutant
ComponentsGeneral control protein GCN4
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


protein localization to nuclear periphery / 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 / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II ...protein localization to nuclear periphery / 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 / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOshaben, K.M. / Horne, W.S.
CitationJournal: Biomacromolecules / Year: 2014
Title: Tuning assembly size in Peptide-based supramolecular polymers by modulation of subunit association affinity.
Authors: Oshaben, K.M. / Horne, W.S.
History
DepositionNov 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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: General control protein GCN4
B: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)8,0872
Polymers8,0872
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-19 kcal/mol
Surface area4720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.199, 30.410, 27.788
Angle α, β, γ (deg.)90.00, 102.01, 90.00
Int Tables number5
Space group name H-MC121
Detailsbiological unit is asymmetric unit

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Components

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


Mass: 4043.736 Da / Num. of mol.: 2 / Fragment: unp residues 249-281 / Mutation: V9I / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P03069
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M sodium acetate, 0.1 M sodium citrate tribasic dihydrate, 25% w/v PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 23, 2012 / Details: Rigaku VariMax Optics
RadiationMonochromator: Rigaku VariMax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40.96 Å / Num. obs: 5462 / % possible obs: 99.3 % / Redundancy: 3.29 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZTA

2zta


Resolution: 1.9→27.179 Å / SU ML: 0.32 / σ(F): 1.4 / Phase error: 32.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2829 245 4.5 %
Rwork0.2581 --
obs0.2593 5447 99.07 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.951 Å2 / ksol: 0.425 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.5347 Å20 Å22.488 Å2
2---1.5795 Å2-0 Å2
3----4.9552 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms529 0 0 20 549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003540
X-RAY DIFFRACTIONf_angle_d0.657718
X-RAY DIFFRACTIONf_dihedral_angle_d16.187224
X-RAY DIFFRACTIONf_chiral_restr0.03881
X-RAY DIFFRACTIONf_plane_restr0.00292

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