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- PDB-1unx: Structure Based Engineering of Internal Molecular Surfaces Of Fou... -

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Basic information

Entry
Database: PDB / ID: 1unx
TitleStructure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsFOUR HELIX BUNDLE / CAVITY
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: 2.4 Å
AuthorsYadav, M.K. / Redman, J.E. / Alvarez-Gutierrez, J.M. / Zhang, Y. / Stout, C.D. / Ghadiri, M.R.
CitationJournal: Biochemistry / Year: 2005
Title: Structure-Based Engineering of Internal Cavities in Coiled-Coil Peptides
Authors: Yadav, M.K. / Redman, J.E. / Leman, L.J. / Alvarez-Gutierrez, J.M. / Zhang, Y. / Stout, C.D. / Ghadiri, M.R.
History
DepositionSep 15, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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
Water0
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_655-x+7/4,-z+3/4,-y+3/41
MethodPQS
Unit cell
Length a, b, c (Å)78.814, 78.814, 78.814
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein/peptide GENERAL CONTROL PROTEIN GCN4 / GCN4 LEUCINE ZIPPER / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN / PL1


Mass: 4046.757 Da / Num. of mol.: 2 / Mutation: YES / Source method: obtained synthetically
Details: BASED ON SEQUENCE FROM SACCHAROMYCES CEREVISIAE (BAKER'S YEAST)
Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P03069
Compound detailsENGINEERED RESIDUE VAL 271 SER, CHAINS A AND B

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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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 7 / Details: 2.5 M NACL, 100 MM NAAC, 200 MM LI2SO4, pH 7.00

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Data collection

DiffractionMean temperature: 114 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorDate: Oct 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→26.3 Å / Num. obs: 3607 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 18.8 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 3.4

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Processing

Software
NameVersionClassification
REFMACrefinement
CrystalClear(MSC/RIGAKU)data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→55.9 Å / SU B: 9.115 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.295
RfactorNum. reflection% reflectionSelection details
Rfree0.30603 155 4.3 %RANDOM
Rwork0.24619 ---
obs0.2273 3446 99.83 %-
Displacement parametersBiso mean: 46.611 Å2
Refinement stepCycle: LAST / Resolution: 2.4→55.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms539 0 0 0 539

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