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- PDB-1u9h: Heterocyclic Peptide Backbone Modification in GCN4-pLI Based Coil... -

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Basic information

Entry
Database: PDB / ID: 1u9h
TitleHeterocyclic Peptide Backbone Modification in GCN4-pLI Based Coiled Coils: Replacement of E(22)L(23)
ComponentsGeneral control protein GCN4
KeywordsTRANSCRIPTION / tetrameric alpha-helical coiled coil / heterocycic backbone modification
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsHorne, W.S. / Yadav, M.K. / Stout, C.D. / Ghadiri, M.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: Heterocyclic peptide backbone modifications in an alpha-helical coiled coil.
Authors: Horne, W.S. / Yadav, M.K. / Stout, C.D. / Ghadiri, M.R.
History
DepositionAug 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
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

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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)8,0502
Polymers8,0502
Non-polymers00
Water81145
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)16,0994
Polymers16,0994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area6970 Å2
ΔGint-50 kcal/mol
Surface area7030 Å2
MethodPISA, PQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-12 kcal/mol
Surface area5210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.404, 45.404, 90.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-41-

HOH

21B-46-

HOH

DetailsThe tetramer formed by chains A and B is generated by the two fold axis: y,-x,1/4+z

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Components

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


Mass: 4024.800 Da / Num. of mol.: 2 / Mutation: (TA4)22E,A23L / Source method: obtained synthetically
Details: Prepared by Fmoc solid phase peptide synthesis. The sequence of this protein can be found naturally in Saccharomyces cerevisiae (Baker's yeast).
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16 M magnesium acetate tetrahydrate, 0.08 M sodium cacodylate, pH 6.5, 16% w/v PEG 8000, 20% v/v anhydrous glycerol, 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: Apr 8, 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: 2.17→45.17 Å / Num. obs: 5435 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 7.2
Reflection shellResolution: 2.17→2.25 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→45.17 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.418 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28418 244 4.5 %RANDOM
Rwork0.24687 ---
all0.24857 ---
obs0.24857 5190 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.136 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.17→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms527 0 0 45 572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022531
X-RAY DIFFRACTIONr_bond_other_d0.0020.02529
X-RAY DIFFRACTIONr_angle_refined_deg2.0012.059703
X-RAY DIFFRACTIONr_angle_other_deg1.02331235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.88560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.11124.78323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.45115124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.172154
X-RAY DIFFRACTIONr_chiral_restr0.1050.279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02542
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0290
X-RAY DIFFRACTIONr_nbd_refined0.240.2142
X-RAY DIFFRACTIONr_nbd_other0.2170.2558
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2245
X-RAY DIFFRACTIONr_nbtor_other0.1020.2358
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.229
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9241.5339
X-RAY DIFFRACTIONr_mcbond_other0.211.5127
X-RAY DIFFRACTIONr_mcangle_it1.5352487
X-RAY DIFFRACTIONr_scbond_it2.3613240
X-RAY DIFFRACTIONr_scangle_it3.7324.5214
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 18 -
Rwork0.227 352 -
obs--94.63 %

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