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

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Basic information

Entry
Database: PDB / ID: 6olo
TitleControlling the Self-Assembly of Synthetic Metal-Coordinating Coiled-Coil Peptides: Hexagonal 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: 2.3 Å
AuthorsSchieb, 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 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Designed trimeric coiled coil peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2392
Polymers3,1761
Non-polymers641
Water1086
1
A: Designed trimeric coiled coil peptide
hetero molecules

A: Designed trimeric coiled coil peptide
hetero molecules

A: 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
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3580 Å2
ΔGint-48 kcal/mol
Surface area5810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.739, 39.739, 41.945
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein/peptide Designed trimeric coiled coil peptide


Mass: 3175.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 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: Jan 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→26.61 Å / Num. obs: 1094 / % possible obs: 100 % / Redundancy: 5.25 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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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, CHAIN A

4dzl


Resolution: 2.3→19.87 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2.19 / Phase error: 28.95
RfactorNum. reflection% reflection
Rfree0.273 110 10.07 %
Rwork0.257 --
obs0.259 1092 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms212 0 1 6 219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004217
X-RAY DIFFRACTIONf_angle_d0.968294
X-RAY DIFFRACTIONf_dihedral_angle_d20.304127
X-RAY DIFFRACTIONf_chiral_restr0.03435
X-RAY DIFFRACTIONf_plane_restr0.00233
LS refinement shellResolution: 2.3011→2.38 Å
RfactorNum. reflection% reflection
Rfree0.2733 110 -
Rwork0.2565 982 -
obs--100 %

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