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- PDB-5w0j: Antiparallel coiled coil hexamer formed by de novo peptides (ACC-... -

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Basic information

Entry
Database: PDB / ID: 5w0j
TitleAntiparallel coiled coil hexamer formed by de novo peptides (ACC-Hex2).
Componentspeptide 1
KeywordsDE NOVO PROTEIN / antiparallel / hexamer / de novo / phe-ile zipper
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.201 Å
AuthorsSpencer, R.K. / Hochbaum, A.I.
CitationJournal: Biochemistry / Year: 2017
Title: The Phe-Ile Zipper: A Specific Interaction Motif Drives Antiparallel Coiled-Coil Hexamer Formation.
Authors: Spencer, R.K. / Hochbaum, A.I.
History
DepositionMay 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Dec 14, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_rmsd_bond / struct_asym / struct_conf / struct_conn / struct_ref_seq
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_alt_id / _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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: peptide 1
B: peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9133
Polymers6,8782
Non-polymers351
Water19811
1
A: peptide 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)20,84512
Polymers20,6336
Non-polymers2136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area12130 Å2
ΔGint-158 kcal/mol
Surface area8770 Å2
MethodPISA
2
B: peptide 1
x 6


Theoretical massNumber of molelcules
Total (without water)20,6336
Polymers20,6336
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area11560 Å2
ΔGint-109 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.560, 52.560, 93.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-101-

CL

21B-203-

HOH

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Components

#1: Protein/peptide peptide 1


Mass: 3438.790 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 1.87 Å3/Da / Density % sol: 34.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M sodium formate pH 6.5, 35% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2016
RadiationMonochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.201→40.89 Å / Num. obs: 5328 / % possible obs: 99.51 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.04 / Net I/σ(I): 13.9
Reflection shellResolution: 2.201→2.29 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 300 / CC1/2: 0.96 / Rpim(I) all: 0.11 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.201→40.887 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.63
RfactorNum. reflection% reflection
Rfree0.2769 475 9.77 %
Rwork0.2195 --
obs0.2253 4864 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.94 Å2
Refinement stepCycle: LAST / Resolution: 2.201→40.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms454 0 21 11 486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003509
X-RAY DIFFRACTIONf_angle_d0.761678
X-RAY DIFFRACTIONf_dihedral_angle_d16.802316
X-RAY DIFFRACTIONf_chiral_restr0.13171
X-RAY DIFFRACTIONf_plane_restr0.00188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.201-2.51950.25981570.22061479X-RAY DIFFRACTION100
2.5195-3.17410.27061570.24521446X-RAY DIFFRACTION100
3.1741-40.89440.28511610.20711464X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.54780.2025-0.85023.1878-1.34945.4861-0.0566-0.24750.0190.08680.03610.04971.6490.99590.43980.48940.01160.07680.28110.02360.4815-0.401421.31817.0502
21.4613-0.1161-2.09061.3031-0.3553.1914-0.51670.01690.1911-0.0093-0.38160.3202-1.5897-0.2258-0.18240.41620.0025-0.15680.1411-0.00410.40450.40259.14980.2701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 29 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 29 )

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