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- PDB-2ahp: GCN4 leucine zipper, mutation of Lys15 to epsilon-azido-Lys -

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Basic information

Entry
Database: PDB / ID: 2ahp
TitleGCN4 leucine zipper, mutation of Lys15 to epsilon-azido-Lys
ComponentsGeneral control protein GCN4
KeywordsDE NOVO PROTEIN / GCN4 / coiled coil / azide
Function / homology
Function and homology information


protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / 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
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHorne, W.S. / Ghadiri, M.R.
CitationJournal: To be Published
Title: GCN4 leucine zipper, mutation of Lys15 to epsilon-azido-Lys
Authors: Horne, W.S. / Ghadiri, M.R.
History
DepositionJul 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 10, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)8,1702
Polymers8,1702
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-19 kcal/mol
Surface area4980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.162, 30.397, 21.716
Angle α, β, γ (deg.)90.00, 95.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-53-

HOH

Detailsthe asymmetric unit comprises the putative biological assembly

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Components

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


Mass: 4084.810 Da / Num. of mol.: 2 / Fragment: residues 249-281 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P03069
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.065 M Tris, 5.2% w/v PEG 8000, 35% v/v anhydrous glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 2004 / Details: osmic confocal mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→29.08 Å / Num. obs: 4473 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.49 % / Rmerge(I) obs: 0.036 / Χ2: 0.24 / Net I/σ(I): 10.6 / Scaling rejects: 119
Reflection shellResolution: 2→2.07 Å / % possible obs: 98 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.4 / Num. measured obs: 23 / Χ2: 0.28 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
CrystalClear(MSC/RIGAKU)data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.08 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.878 / SU B: 4.825 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 204 4.6 %RANDOM
Rwork0.189 ---
all0.192 ---
obs0.192 4472 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.043 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.77 Å2
2--0.45 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms544 0 0 65 609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021546
X-RAY DIFFRACTIONr_bond_other_d0.0010.02519
X-RAY DIFFRACTIONr_angle_refined_deg1.2042.028725
X-RAY DIFFRACTIONr_angle_other_deg0.7831206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.588565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11125.71428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94215112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.931154
X-RAY DIFFRACTIONr_chiral_restr0.0680.281
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0293
X-RAY DIFFRACTIONr_nbd_refined0.2060.2117
X-RAY DIFFRACTIONr_nbd_other0.1710.2446
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2247
X-RAY DIFFRACTIONr_nbtor_other0.0820.2317
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4550.215
X-RAY DIFFRACTIONr_mcbond_it0.8411.5361
X-RAY DIFFRACTIONr_mcbond_other0.1591.5136
X-RAY DIFFRACTIONr_mcangle_it1.1962520
X-RAY DIFFRACTIONr_scbond_it2.5493227
X-RAY DIFFRACTIONr_scangle_it4.0964.5205
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 21 -
Rwork0.241 300 -
all-321 -
obs--97.57 %

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