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- PDB-5u59: Coiled Coil Peptide Metal Coordination Framework: Dimer Fold Grow... -

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Basic information

Entry
Database: PDB / ID: 5u59
TitleCoiled Coil Peptide Metal Coordination Framework: Dimer Fold Grown with Citrate
ComponentsDesigned dimeric coiled coil peptide with two terpyridine side chains
KeywordsDE NOVO PROTEIN / designed peptide / synthetic / metal coordination framework / supramolecular assembly
Function / homologyCITRIC ACID / COPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTavenor, N.A. / Murnin, M.J. / Horne, W.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR1149067 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Supramolecular Metal-Coordination Polymers, Nets, and Frameworks from Synthetic Coiled-Coil Peptides.
Authors: Tavenor, N.A. / Murnin, M.J. / Horne, W.S.
History
DepositionDec 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 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

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Assembly

Deposited unit
A: Designed dimeric coiled coil peptide with two terpyridine side chains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0965
Polymers3,5841
Non-polymers5114
Water48627
1
A: Designed dimeric coiled coil peptide with two terpyridine side chains
hetero molecules

A: Designed dimeric coiled coil peptide with two terpyridine side chains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,19110
Polymers7,1682
Non-polymers1,0238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area3110 Å2
ΔGint-50 kcal/mol
Surface area6050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.326, 52.170, 25.581
Angle α, β, γ (deg.)90.00, 103.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Designed dimeric coiled coil peptide with two terpyridine side chains


Mass: 3584.174 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.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.34 Å3/Da / Density % sol: 63.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M sodium citrate pH 6.0, 15% w/v PEG 4000, 3 mM copper(II) chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→29.21 Å / Num. obs: 2391 / % possible obs: 99.6 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 29
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.42 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3.8 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DZM

4dzm


Resolution: 2.2→26.09 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 25.85
RfactorNum. reflection% reflection
Rfree0.257 238 10.03 %
Rwork0.226 --
obs0.229 2374 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→26.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms252 0 28 27 307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003293
X-RAY DIFFRACTIONf_angle_d1.068400
X-RAY DIFFRACTIONf_dihedral_angle_d30.93105
X-RAY DIFFRACTIONf_chiral_restr0.02836
X-RAY DIFFRACTIONf_plane_restr0.00247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.77150.3371190.29051056X-RAY DIFFRACTION99
2.7715-26.08680.2341190.20551080X-RAY DIFFRACTION99

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