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- PDB-2ccn: pLI E20C is antiparallel -

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Basic information

Entry
Database: PDB / ID: 2ccn
TitlepLI E20C is antiparallel
ComponentsGeneral control protein GCN4
KeywordsFOUR HELIX BUNDLE / ANTIPARALLEL / PARALLEL / PLI / DNA-BINDING / NUCLEAR PROTEIN / TRANSCRIPTION / TRANSCRIPTION REGULATION / ACTIVATOR / AMINO-ACID BIOSYNTHESIS
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: 1.6 Å
AuthorsYadav, M.K. / Leman, L.J. / Price, D.J. / Brooks 3rd, C.L. / Stout, C.D. / Ghadiri, M.R.
CitationJournal: Biochemistry / Year: 2006
Title: Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent- ...Title: Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution.
Authors: Yadav, M.K. / Leman, L.J. / Price, D.J. / Brooks 3rd, C.L. / Stout, C.D. / Ghadiri, M.R.
History
DepositionJan 16, 2006Deposition site: PDBE / Processing site: PDBE
SupersessionApr 6, 2006ID: 1VZL
Revision 1.0Apr 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 19, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_nat / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.src_method / _entity_name_com.name
Revision 1.4Nov 7, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.name / _citation_author.name / _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)8,0942
Polymers8,0942
Non-polymers00
Water1,49583
1
A: General control protein GCN4
B: General control protein GCN4

A: General control protein GCN4
B: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)16,1874
Polymers16,1874
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.388, 35.384, 104.318
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-2020-

HOH

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Components

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


Mass: 4046.866 Da / Num. of mol.: 2 / Fragment: RESIDUES 249-281 / Mutation: YES / 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.: 83 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 268 TO CYS ENGINEERED RESIDUE IN CHAIN B, GLU 268 TO CYS

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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: 1.93 Å3/Da / Density % sol: 35 %
Crystal growpH: 10.5 / Details: 100MM CAPS PH 10.5, 30% PEG 400

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: ADSC CCD / Detector: CCD / Date: May 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→34.77 Å / Num. obs: 9395 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.29 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 27.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→51.99 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.572 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.108 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N TERMINUS OF PEPTIDE IS ACETYLATED WITH ACETIC ANHYDRIDE.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 447 4.8 %RANDOM
Rwork0.217 ---
obs0.219 8913 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--0.66 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.6→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms520 0 0 83 603
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.452 35
Rwork0.377 605

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