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- PDB-5eon: Crystal structure of a de novo antiparallel coiled-coil hexamer -... -

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Basic information

Entry
Database: PDB / ID: 5eon
TitleCrystal structure of a de novo antiparallel coiled-coil hexamer - ACC-Hex
ComponentsACC-Hex
KeywordsDE NOVO PROTEIN / hexamer / coiled-coil / antiparallel
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 Å
AuthorsSpencer, R.K. / Hochbaum, A.I.
CitationJournal: Biochemistry / Year: 2016
Title: X-ray Crystallographic Structure and Solution Behavior of an Antiparallel Coiled-Coil Hexamer Formed by de Novo Peptides.
Authors: Spencer, R.K. / Hochbaum, A.I.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
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 / chem_comp ...atom_site / chem_comp / citation / database_2 / entity / entity_poly / entity_poly_seq / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / 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_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.type / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_oper_list.symmetry_operation / _struct_conf.end_auth_comp_id / _struct_conf.end_label_comp_id / _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_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
Revision 2.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACC-Hex
B: ACC-Hex
C: ACC-Hex


Theoretical massNumber of molelcules
Total (without water)10,0563
Polymers10,0563
Non-polymers00
Water1,820101
1
A: ACC-Hex
B: ACC-Hex
C: ACC-Hex

A: ACC-Hex
B: ACC-Hex
C: ACC-Hex


Theoretical massNumber of molelcules
Total (without water)20,1126
Polymers20,1126
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11130 Å2
ΔGint-110 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.256, 59.256, 52.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11C-119-

HOH

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Components

#1: Protein/peptide ACC-Hex


Mass: 3351.995 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1 M Na formate, pH 7.3, PEG 3350 29%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.696→32.754 Å / Num. obs: 10805 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 31.7
Reflection shellResolution: 1.696→1.757 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.42 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EOJ

5eoj


Resolution: 1.696→32.754 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 1080 10 %
Rwork0.198 --
obs0.2003 10797 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.696→32.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms717 0 0 101 818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002786
X-RAY DIFFRACTIONf_angle_d0.3891054
X-RAY DIFFRACTIONf_dihedral_angle_d19.116476
X-RAY DIFFRACTIONf_chiral_restr0.035107
X-RAY DIFFRACTIONf_plane_restr0.001134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6963-1.77350.28131270.25231145X-RAY DIFFRACTION97
1.7735-1.8670.26761330.22411195X-RAY DIFFRACTION100
1.867-1.98390.24471330.2431199X-RAY DIFFRACTION100
1.9839-2.13710.22331330.19271196X-RAY DIFFRACTION100
2.1371-2.35210.22781340.18371203X-RAY DIFFRACTION100
2.3521-2.69230.20781360.18061224X-RAY DIFFRACTION100
2.6923-3.39150.19021370.18021235X-RAY DIFFRACTION100
3.3915-32.75970.23451470.20951320X-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)
12.7344-0.81480.71393.9031-1.23612.7352-0.142-0.0308-0.01740.0895-0.0213-0.2952-0.21820.46510.18720.1197-0.02220.00370.14520.07870.3041-5.8328-13.06191.2028
22.04611.0153-1.76982.3988-0.91624.2903-0.1391-0.0756-0.23970.29520.0855-0.0450.14190.31850.16230.12160.03680.02070.13940.06740.321-7.8566-19.8851-1.9469
33.3639-0.5468-1.69261.79081.38312.6650.02850.1676-0.17430.18730.14420.01670.5308-0.24730.12960.183-0.0141-0.0120.11750.06510.3187-17.43-22.7321.2605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2 through 29 )
3X-RAY DIFFRACTION3chain 'C' and (resid 2 through 29 )

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