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- PDB-5u5a: Coiled Coil Peptide Metal Coordination Framework: Dimer Fold -

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Basic information

Entry
Database: PDB / ID: 5u5a
TitleCoiled Coil Peptide Metal Coordination Framework: Dimer Fold
ComponentsDesigned dimeric coiled coil peptide with two terpyridine side chains
KeywordsDE NOVO PROTEIN / designed peptide / synthetic / metal coordination framework / supramolecular assembly
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 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 / 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_asym_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_asym_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_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.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 1.4Nov 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)3,7113
Polymers3,5841
Non-polymers1272
Water362
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)7,4236
Polymers7,1682
Non-polymers2544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area2400 Å2
ΔGint-42 kcal/mol
Surface area5740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.141, 57.141, 80.185
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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 / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 5.37 Å3/Da / Density % sol: 77.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M BIS-TRIS with 2 mM terephthalic acid pH 6.5, 10 mM copper(II) chloride, 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.23→31.15 Å / Num. obs: 1430 / % possible obs: 99.6 % / Redundancy: 7.67 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 11
Reflection shellResolution: 3.23→3.35 Å / Redundancy: 8.15 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DZM

4dzm


Resolution: 3.23→31.15 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 38.97
RfactorNum. reflection% reflection
Rfree0.313 141 10.07 %
Rwork0.299 --
obs0.3 1400 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.23→31.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms256 0 2 2 260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005273
X-RAY DIFFRACTIONf_angle_d1.288371
X-RAY DIFFRACTIONf_dihedral_angle_d28.8996
X-RAY DIFFRACTIONf_chiral_restr0.03236
X-RAY DIFFRACTIONf_plane_restr0.00642
Refinement TLS params.Method: refined / Origin x: 22.4171 Å / Origin y: -14.1121 Å / Origin z: -2.4391 Å
111213212223313233
T1.3679 Å2-0.2522 Å20.0932 Å2-1.1924 Å20.0761 Å2--0.6616 Å2
L9.8697 °2-2.8847 °22.7255 °2-7.1323 °2-1.1187 °2--9.3164 °2
S0.584 Å °-1.8292 Å °0.236 Å °-0.1561 Å °-0.8653 Å °-0.2957 Å °0.6444 Å °0.5096 Å °0.3046 Å °
Refinement TLS groupSelection details: CHAIN 'A' AND (RESID 0 THROUGH 30 )

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