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- PDB-6oln: Controlling the Self-Assembly of Synthetic Metal-Coordinating Coi... -

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Basic information

Entry
Database: PDB / ID: 6oln
TitleControlling the Self-Assembly of Synthetic Metal-Coordinating Coiled-Coil Peptides: Orthorhombic Lattice from a Trimeric Coiled Coil
ComponentsDesigned trimeric coiled coil peptide
KeywordsDE NOVO PROTEIN / metal coordination framework / supramolecular assembly
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsScheib, K.A. / Horne, W.S.
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Understanding and controlling the metal-directed assembly of terpyridine-functionalized coiled-coil peptides.
Authors: Scheib, K.A. / Tavenor, N.A. / Lawless, M.J. / Saxena, S. / Horne, W.S.
History
DepositionApr 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.conn_type_id / _struct_conn.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
Revision 1.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Designed trimeric coiled coil peptide
B: Designed trimeric coiled coil peptide
C: Designed trimeric coiled coil peptide
D: Designed trimeric coiled coil peptide
E: Designed trimeric coiled coil peptide
F: Designed trimeric coiled coil peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,64918
Polymers19,0556
Non-polymers59412
Water1,946108
1
A: Designed trimeric coiled coil peptide
B: Designed trimeric coiled coil peptide
C: Designed trimeric coiled coil peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,93112
Polymers9,5273
Non-polymers4039
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Designed trimeric coiled coil peptide
E: Designed trimeric coiled coil peptide
F: Designed trimeric coiled coil peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7186
Polymers9,5273
Non-polymers1913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.783, 50.962, 79.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-206-

HOH

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Components

#1: Protein/peptide
Designed trimeric coiled coil peptide


Mass: 3175.832 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3350, 5 mM copper(II) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→41.545 Å / Num. obs: 7260 / % possible obs: 99.9 % / Redundancy: 3.68 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 18
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 11.6 / Num. unique obs: 718 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DZL

4dzl


Resolution: 2.5→41.55 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.53
RfactorNum. reflection% reflection
Rfree0.295 726 10.06 %
Rwork0.268 --
obs0.271 7220 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 0 12 108 1476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041386
X-RAY DIFFRACTIONf_angle_d0.8841872
X-RAY DIFFRACTIONf_dihedral_angle_d12.952822
X-RAY DIFFRACTIONf_chiral_restr0.036216
X-RAY DIFFRACTIONf_plane_restr0.002216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.69310.36271410.29091279X-RAY DIFFRACTION99
2.6931-2.9640.3131400.30111261X-RAY DIFFRACTION100
2.964-3.39280.29351410.29271295X-RAY DIFFRACTION100
3.3928-4.27390.29671500.24911298X-RAY DIFFRACTION100
4.2739-41.55080.25721540.24511361X-RAY DIFFRACTION99

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