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- PDB-1w5g: An anti-parallel four helix bundle (acetimide modification). -

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Basic information

Entry
Database: PDB / ID: 1w5g
TitleAn anti-parallel four helix bundle (acetimide modification).
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsSTRUCTURAL PROTEIN / FOUR 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: 2.16 Å
AuthorsYadav, M.K. / Leman, L.J. / 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
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)8,0422
Polymers8,0422
Non-polymers00
Water362
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)16,0834
Polymers16,0834
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area5550 Å2
ΔGint-85.99 kcal/mol
Surface area7120 Å2
MethodPISA
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 ACETIMIDE


Mass: 4020.829 Da / Num. of mol.: 2 / Mutation: YES / Source method: obtained synthetically
Details: PEPTIDE REACTED WITH IODOACETIMIDE TO YEILD THIOETHER FROM CYSTEINE. NOTE SHIFT IN TYROSINE POSITION FROM PDB ENTRY 1VZL
Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P03069
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION GLU 268 CYS THE N-TERMINUS OF THIS PEPTIDE IS ACETYLATED.

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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
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: May 29, 2004 / Details: CONFOCAL
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.16→34.88 Å / Num. obs: 3960 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.37 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.3
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 5.01 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.5 / % possible all: 97.6

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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: 2.16→51.99 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.853 / SU B: 6.182 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.337 176 4.5 %RANDOM
Rwork0.304 ---
obs0.305 3754 99.4 %-
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: 40.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å20 Å2
2--1.16 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 2.16→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms491 0 0 2 493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021493
X-RAY DIFFRACTIONr_bond_other_d0.0020.02494
X-RAY DIFFRACTIONr_angle_refined_deg1.5262.026655
X-RAY DIFFRACTIONr_angle_other_deg0.87631145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.729562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.281
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02510
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0279
X-RAY DIFFRACTIONr_nbd_refined0.2090.2154
X-RAY DIFFRACTIONr_nbd_other0.2180.2505
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1940.2470
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2850.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.020.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8911.5317
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6552501
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4373176
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0934.5154
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.22 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 10
Rwork0.229 268

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