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Entry
Database: PDB / ID: 1l4x
TitleOctameric de novo designed peptide
ComponentsSIN-ASP-GLU-LEU-GLU-ARG-ALA-ILE-ARG-GLU-LEU-ALA-ALA-ARG-ILE-LYS-NH2
KeywordsDE NOVO PROTEIN / coiled coil / protein de novo design / ionic interactions / protein folding / protein oligomerization
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2 Å
AuthorsMeier, M. / Lustig, A. / Aebi, U. / Burkhard, P.
Citation
Journal: J.STRUCT.BIOL. / Year: 2002
Title: Removing an interhelical salt bridge abolishes coiled-coil formation in a de novo designed peptide
Authors: Meier, M. / Lustig, A. / Aebi, U. / Burkhard, P.
#1: Journal: To be Published
Title: Improving coiled-coil stability by optimizing ionic interactions
Authors: Burkhard, P. / Ivaninskii, S. / Lustig, A.
#2: Journal: Protein Sci. / Year: 2000
Title: Design of a Minimal Protein Oligomerization Domain by a Structural Approach
Authors: Burkhard, P. / Meier, M. / Lustig, A.
#3: Journal: Structure / Year: 2000
Title: The Coiled-coil Trigger Site of the Rod Domain of Cortexillin I Unveils a Distinct Network of Interhelical and Intrahelical Salt Bridges
Authors: Burkhard, P. / Kammerer, R.A. / Steinmetz, M.O. / Bourenkov, G.P. / Aebi, U.
History
DepositionMar 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jun 7, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_poly / entity_poly_seq / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct / struct_asym / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct.title / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 3.0Apr 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end
Revision 3.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 400COMPOUND THE PEPTIDE DOES NOT FORM A COILED COIL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIN-ASP-GLU-LEU-GLU-ARG-ALA-ILE-ARG-GLU-LEU-ALA-ALA-ARG-ILE-LYS-NH2
B: SIN-ASP-GLU-LEU-GLU-ARG-ALA-ILE-ARG-GLU-LEU-ALA-ALA-ARG-ILE-LYS-NH2
C: SIN-ASP-GLU-LEU-GLU-ARG-ALA-ILE-ARG-GLU-LEU-ALA-ALA-ARG-ILE-LYS-NH2
D: SIN-ASP-GLU-LEU-GLU-ARG-ALA-ILE-ARG-GLU-LEU-ALA-ALA-ARG-ILE-LYS-NH2
E: SIN-ASP-GLU-LEU-GLU-ARG-ALA-ILE-ARG-GLU-LEU-ALA-ALA-ARG-ILE-LYS-NH2
F: SIN-ASP-GLU-LEU-GLU-ARG-ALA-ILE-ARG-GLU-LEU-ALA-ALA-ARG-ILE-LYS-NH2
G: SIN-ASP-GLU-LEU-GLU-ARG-ALA-ILE-ARG-GLU-LEU-ALA-ALA-ARG-ILE-LYS-NH2
H: SIN-ASP-GLU-LEU-GLU-ARG-ALA-ILE-ARG-GLU-LEU-ALA-ALA-ARG-ILE-LYS-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,14110
Polymers15,0818
Non-polymers602
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.628, 56.628, 113.869
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11E-25-

HOH

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Components

#1: Protein/peptide
SIN-ASP-GLU-LEU-GLU-ARG-ALA-ILE-ARG-GLU-LEU-ALA-ALA-ARG-ILE-LYS-NH2


Mass: 1885.150 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: This peptide is a de novo designed sequence. / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.6966.67
2
3
Crystal grow
Crystal-IDMethodpHDetails
1vapor diffusion, hanging drop4.6magnesium sulphate; sodium acetate or bicine, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 100K
2vapor diffusion, hanging drop4.6magnesium sulphate; sodium acetate or bicine, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 100K
3vapor diffusion, hanging drop9magnesium sulphate; sodium acetate or bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal grow
*PLUS
pH: 9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMBicine1reservoirpH9.0
260 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODEELLIOTT GX-2011.54181.5418
ROTATING ANODEELLIOTT GX-2021.54181.5418
SYNCHROTRONESRF ID2930.9762570.976257
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEFeb 23, 2001
MARRESEARCH2IMAGE PLATEMar 9, 2001
ADSC QUANTUM 43CCDJul 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.9762571
ReflectionResolution: 2→50 Å / Num. all: 14920 / Num. obs: 14176 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 13.2
Reflection shellResolution: 2→2.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1004 / % possible all: 83.3
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 96.4 %
Reflection shell
*PLUS
% possible obs: 83.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
SHARPphasing
CNSrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: SIR / Resolution: 2→30.02 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: maximum likelihood target using amplitudes. The CG, CD, CE and NZ of LYS 15 in chains C and G are missing in the coordinates because they are disordered.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 711 5.1 %RANDOM
Rwork0.242 ---
all-14176 --
obs-13923 93.5 %-
Solvent computationSolvent model: flat model / Bsol: 92.7455 Å2 / ksol: 0.414419 e/Å3
Displacement parametersBiso mean: 55 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å2-3.43 Å20 Å2
2--0.72 Å20 Å2
3----1.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 58 105 1163
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d16.1
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it5.721.5
X-RAY DIFFRACTIONc_mcangle_it7.662
X-RAY DIFFRACTIONc_scbond_it7.892
X-RAY DIFFRACTIONc_scangle_it11.272.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.49 107 5.6 %
Rwork0.454 1815 -
obs-1922 79.6 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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