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- PDB-2bni: pLI mutant E20C L16G Y17H, antiparallel -

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Basic information

Entry
Database: PDB / ID: 2bni
TitlepLI mutant E20C L16G Y17H, antiparallel
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsFOUR HELIX BUNDLE / ANTIPARALLEL FOUR HELIX BUNDLE ACYL TRANSFERASE
Function / homology
Function and homology information


FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process ...FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor 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 / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
General control transcription factor GCN4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionMar 24, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2005Provider: 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 / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4
C: GENERAL CONTROL PROTEIN GCN4
D: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)16,4034
Polymers16,4034
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)25.814, 25.814, 148.595
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein/peptide
GENERAL CONTROL PROTEIN GCN4 / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN / PLI E20C N16G Y17H


Mass: 4100.854 Da / Num. of mol.: 4 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P03069
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.8 Å3/Da / Density % sol: 30.6 %
Crystal growMethod: vapor diffusion, sitting drop
Details: SITTING DROP WITH 200NL 20% PEG 3350 0.2M POTASSIUM THIOCYANATE AND 200NL 20MG/ML PEPTIDE STOCK IN WATER.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97
DetectorDate: Dec 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 89229 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 5.17 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.65

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→149.07 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MAPS WERE VERY SHARP AND ABA GROUPS WERE CLEAR. R FACTOR A LITTLE HIGHER THAN EXPECTED, ALTHOUGH CONSISTENT WITH OTHER STRUCTURES. SPOTS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MAPS WERE VERY SHARP AND ABA GROUPS WERE CLEAR. R FACTOR A LITTLE HIGHER THAN EXPECTED, ALTHOUGH CONSISTENT WITH OTHER STRUCTURES. SPOTS WERE A LITTLE STREAKY WITH AN ICE RING, BUT DATA ENDED UP PROCESSING WELL.THIS PEPTIDE IS AN ACTIVE AMINOACYL TRANSFERASE AND WILL HOPEFULLY BE FOUND TO HAVE SOME SORT OF BINDING AND CATALYTIC ABILITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 873 5.1 %RANDOM
Rwork0.237 ---
obs0.239 16376 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20.61 Å20 Å2
2--1.22 Å20 Å2
3----1.83 Å2
Refinement stepCycle: LAST / Resolution: 1.5→149.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1022 0 0 55 1077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211043
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0712.0261379
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1895126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.35225.6141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93715232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.267155
X-RAY DIFFRACTIONr_chiral_restr0.1290.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02721
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.2467
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2743
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3411.5647
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12721027
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5343396
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7914.5352
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.273 53
Rwork0.223 917

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