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- PDB-1w5h: An anti-parallel four helix bundle. -

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Basic information

Entry
Database: PDB / ID: 1w5h
TitleAn anti-parallel four helix bundle.
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsFOUR HELIX BUNDLE / ANTIPARALLEL FOUR HELIX BUNDLE
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: 2.5 Å
AuthorsYadav, M.K. / Leman, L.J. / 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, C.L. / Stout, C.D. / Ghadiri, M.R.
History
DepositionAug 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval

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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)7,9922
Polymers7,9922
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)15,9834
Polymers15,9834
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.238, 35.238, 104.647
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein/peptide GENERAL CONTROL PROTEIN GCN4 / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN / PLI E20C Y17H


Mass: 3995.802 Da / Num. of mol.: 2 / Mutation: YES / Source method: obtained synthetically
Details: PEPTIDE IS CAPPED WITH PARA ACETAMIDO BENZOIC ACID.
Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P03069
Compound detailsCHAIN A, B ENGINEERED MUTATION TYR 265 HIS, GLU 268 CYS THE N-TERMINUS OF THIS PEPTIDE IS CAPPED ...CHAIN A, B ENGINEERED MUTATION TYR 265 HIS, GLU 268 CYS THE N-TERMINUS OF THIS PEPTIDE IS CAPPED WITH ABA. DATA EXHIBITED SOME EPITAXIAL TWINNING, SLIGHTLY HIGH RFREE.

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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 Å3/Da / Density % sol: 38.9 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 10.5
Details: HANGING DROP, 1UL OF 1MG/ML PEPTIDE IN WATER, 1UL 100MM CAPS, 30% PEG 400, PH 10.5.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorDate: Jun 26, 2004
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→35.41 Å / Num. obs: 3786 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.06 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.11 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35.41 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.873 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.563 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N TERMINUS IS CAPPED WITH ABA.
RfactorNum. reflection% reflectionSelection details
Rfree0.344 116 4.4 %RANDOM
Rwork0.28 ---
obs0.282 2517 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2.5→35.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms450 0 0 0 450
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.304 8
Rwork0.3 177

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