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- PDB-7p3h: Peptide HC02 - Lanthanide Selectivity Engineered into Structurall... -

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Basic information

Entry
Database: PDB / ID: 7p3h
TitlePeptide HC02 - Lanthanide Selectivity Engineered into Structurally Characterized Designed Coiled Coils
ComponentsPeptide HC02
KeywordsMETAL BINDING PROTEIN / lanthanide / de novo / coiled coil / peptide design
Function / homologyTERBIUM(III) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWhite, S.A. / Peacock, A.F.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Defence Science and Technology Laboratory (DSTL) United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Location-Dependent Lanthanide Selectivity Engineered into Structurally Characterized Designed Coiled Coils.
Authors: Slope, L.N. / Daubney, O.J. / Campbell, H. / White, S.A. / Peacock, A.F.A.
History
DepositionJul 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / diffrn_source / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide HC02
B: Peptide HC02
C: Peptide HC02
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1289
Polymers12,4553
Non-polymers6736
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Tb-binding assay, data fit to a 3:1 (peptide:Tb) model
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-121 kcal/mol
Surface area7690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.040, 103.040, 46.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein/peptide Peptide HC02


Mass: 4151.735 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Tb
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.4 Å3/Da / Density % sol: 72 % / Description: Rectangular plate-like crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Drop solution: 16 mg mL-1 synthetic peptide HC02, 6 mM TbCl3 and 5 mM Zn(OAc)2) Reservoir solution: 0.21 M NH4Cl, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.1→41.5 Å / Num. obs: 49925 / % possible obs: 99.93 % / Redundancy: 4.6 % / Biso Wilson estimate: 54.01 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.07557 / Rpim(I) all: 0.03896 / Rrim(I) all: 0.08523 / Net I/σ(I): 13.24
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.4503 / Num. unique obs: 1075 / CC1/2: 0.927 / CC star: 0.981 / R split: 2.76 / Rpim(I) all: 0.2316 / Rrim(I) all: 0.5076 / % possible all: 99.72

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Processing

Software
NameVersionClassification
PHENIXv1.17.1refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished data

Resolution: 2.1→41.5 Å / Cross valid method: THROUGHOUT
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 1132 5.33 %Random
Rwork0.2098 ---
obs0.2109 10818 98.12 %-
Displacement parametersBiso mean: 87.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms879 0 6 68 953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086889
X-RAY DIFFRACTIONf_angle_d1.00761181
X-RAY DIFFRACTIONf_chiral_restr0.0435127
X-RAY DIFFRACTIONf_plane_restr0.0051152
X-RAY DIFFRACTIONf_dihedral_angle_d22.2669359

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