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- PDB-1u9f: Heterocyclic Peptide Backbone Modification in GCN4-pLI Based Coil... -

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Basic information

Entry
Database: PDB / ID: 1u9f
TitleHeterocyclic Peptide Backbone Modification in GCN4-pLI Based Coiled Coils: Replacement of K(15)L(16)
ComponentsGeneral control protein GCN4
KeywordsTRANSCRIPTION / tetrameric alpha-helical coiled coil / heterocycic backbone modification
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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
C: General control protein GCN4
D: General control protein GCN4


Theoretical massNumber of molelcules
Total (without water)16,0994
Polymers16,0994
Non-polymers00
Water1,42379
1
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)16,0994
Polymers16,0994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
2
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 operation8_555-y,-x,-z+1/21
Buried area6940 Å2
ΔGint-59 kcal/mol
Surface area7550 Å2
MethodPISA, PQS
3
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)16,0994
Polymers16,0994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6840 Å2
ΔGint-61 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.599, 67.599, 86.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe tetramer formed by chains A and B is generated by the two fold axis: y,x,-z / The tetramer formed by chains C and D is generated by the two fold axis: 1/2+x,1/2-y,1/4-z

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Components

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


Mass: 4024.734 Da / Num. of mol.: 4 / Mutation: (TA4)15K, L16N / 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.: 79 / 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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.085M HEPES Na, pH7.5, 8.5% v/v isopropanol, 17% w/v PEG4000, 15% 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 30, 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: 2.2→31.49 Å / Num. obs: 10727 / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 7.4
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5

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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: 2.2→31.49 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.859 / SU B: 5.73 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31977 512 4.8 %RANDOM
Rwork0.24925 ---
obs0.25237 10182 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.497 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20 Å2
2---1.08 Å20 Å2
3---2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1081 0 0 79 1160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211089
X-RAY DIFFRACTIONr_bond_other_d0.0140.021066
X-RAY DIFFRACTIONr_angle_refined_deg1.9282.0721445
X-RAY DIFFRACTIONr_angle_other_deg1.01332489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.4725120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03425.29451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.61415246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.469158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021108
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02180
X-RAY DIFFRACTIONr_nbd_refined0.2050.2237
X-RAY DIFFRACTIONr_nbd_other0.1910.21008
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2491
X-RAY DIFFRACTIONr_nbtor_other0.0980.2695
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.8021.5722
X-RAY DIFFRACTIONr_mcbond_other2.8371.5256
X-RAY DIFFRACTIONr_mcangle_it1.78821001
X-RAY DIFFRACTIONr_scbond_it2.8673489
X-RAY DIFFRACTIONr_scangle_it4.4464.5440
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
Rfree0.333 44 -
Rwork0.256 720 -
obs--99.48 %

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