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- PDB-4dme: GCN4 leucine zipper domain in a trimeric oligomerization state -

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Basic information

Entry
Database: PDB / ID: 4dme
TitleGCN4 leucine zipper domain in a trimeric oligomerization state
ComponentsGCN4-p1 leucine zipper domain
KeywordsPROTEIN BINDING
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOshaben, K.M. / Salari, R. / Chong, L.T. / Horne, W.S.
CitationJournal: Biochemistry / Year: 2012
Title: The Native GCN4 Leucine-Zipper Domain Does Not Uniquely Specify a Dimeric Oligomerization State.
Authors: Oshaben, K.M. / Salari, R. / McCaslin, D.R. / Chong, L.T. / Horne, W.S.
History
DepositionFeb 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GCN4-p1 leucine zipper domain
B: GCN4-p1 leucine zipper domain
C: GCN4-p1 leucine zipper domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3776
Polymers12,0893
Non-polymers2883
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-79 kcal/mol
Surface area7200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.179, 34.379, 78.117
Angle α, β, γ (deg.)90.00, 139.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide GCN4-p1 leucine zipper domain


Mass: 4029.709 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Ammonium Sulfate, 0.1 M MES buffer, 30% (w/v) PEG MME 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 2, 2011
RadiationMonochromator: Rigaku VariMax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50.54 Å / Num. obs: 5443 / % possible obs: 99.5 % / Redundancy: 2.71 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.6.0117refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IJ2

1ij2


Resolution: 2.2→50.54 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.891 / Cross valid method: THROUGHOUT / ESU R: 0.381 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28733 244 4.5 %RANDOM
Rwork0.22582 ---
obs0.22856 5198 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.676 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å2-1.78 Å2
2--0.93 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 15 48 891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019857
X-RAY DIFFRACTIONr_bond_other_d00.02612
X-RAY DIFFRACTIONr_angle_refined_deg1.3872.0151145
X-RAY DIFFRACTIONr_angle_other_deg4.04231491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2115103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96524.66745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3115188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.803159
X-RAY DIFFRACTIONr_chiral_restr0.0720.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02926
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02155
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 18 -
Rwork0.265 376 -
obs--100 %

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