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- PDB-1w5j: AN ANTI-PARALLEL FOUR HELIX BUNDLE -

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Basic information

Entry
Database: PDB / ID: 1w5j
TitleAN ANTI-PARALLEL FOUR HELIX BUNDLE
ComponentsGENERAL CONTROL PROTEIN GCN4
KeywordsFOUR HELIX BUNDLE / ANTIPARALLEL FOUR HELIX BUNDLE
Function / homology
Function and homology information


Activation of the AP-1 family of transcription factors / protein localization to nuclear periphery / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / response to amino acid starvation / mediator complex binding / amino acid biosynthetic process / TFIID-class transcription factor complex binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II ...Activation of the AP-1 family of transcription factors / protein localization to nuclear periphery / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / response to amino acid starvation / mediator complex binding / amino acid biosynthetic process / TFIID-class transcription factor complex binding / 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 / transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / DNA-templated transcription / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 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 7, 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 / Derived calculations ...Data collection / Derived calculations / 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 / 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

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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
C: GENERAL CONTROL PROTEIN GCN4
D: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)17,1764
Polymers17,1764
Non-polymers00
Water19811
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)17,1764
Polymers17,1764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
2
C: GENERAL CONTROL PROTEIN GCN4
D: GENERAL CONTROL PROTEIN GCN4

C: GENERAL CONTROL PROTEIN GCN4
D: GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)17,1764
Polymers17,1764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)33.691, 37.192, 103.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 4294.042 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.: 11 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 251 TO LYS ENGINEERED MUTATION IN CHAINS A, B, C, D: ...ENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 251 TO LYS ENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 256 TO LYS ENGINEERED MUTATION IN CHAINS A, B, C, D: CYS 268 TO GLU ENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 275 TO LYS ENGINEERED MUTATION IN CHAINS A, B, C, D: ARG 276 TO LYS
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: 2 Å3/Da / Density % sol: 39 %
Description: BEAM WAS INADVERTENTLY ALIGNED TO CU K BETA EDGE.
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: HANGING DROP, 1 UL OF 10 MG/ML PEPTIDE IN WATER TO 1UL OF 0.07M TRI-SODIUM CITRATE DIHYDRATE PH 5.6 0.7M AMMONIUM DIHYDROGEN PHOSPHATE %30 V/V GLYCEROL, HAMPTON CRYSTAL SCREEN CRYO NUMBER 11

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.3922
DetectorDate: Mar 19, 2003 / Details: CONFOCAL
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3922 Å / Relative weight: 1
ReflectionResolution: 2.2→52 Å / Num. obs: 7116 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.15 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 10.7 / % possible all: 99.3

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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: 2.2→18.6 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.478 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 330 4.7 %RANDOM
Rwork0.228 ---
obs0.231 6718 99.3 %-
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: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→18.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 0 11 1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.0211114
X-RAY DIFFRACTIONr_bond_other_d0.0080.021116
X-RAY DIFFRACTIONr_angle_refined_deg2.3492.0161479
X-RAY DIFFRACTIONr_angle_other_deg1.14732551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1455132
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_restr0.1770.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021215
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02239
X-RAY DIFFRACTIONr_nbd_refined0.2510.2260
X-RAY DIFFRACTIONr_nbd_other0.2780.21207
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0990.2677
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3470.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4530.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6031.5672
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.51721071
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2823442
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.8784.5408
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.304 27
Rwork0.188 460

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