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- PDB-5ehb: A de novo designed hexameric coiled-coil peptide with iodotyrosine -

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Basic information

Entry
Database: PDB / ID: 5ehb
TitleA de novo designed hexameric coiled-coil peptide with iodotyrosine
ComponentspHiosYI
KeywordsDE NOVO PROTEIN / coiled-coil / peptide design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.19 Å
AuthorsLizatovic, R. / Aurelius, O. / Stenstrom, O. / Drakenberg, T. / Akke, M. / Logan, D.T. / Andre, I.
CitationJournal: Structure / Year: 2016
Title: A De Novo Designed Coiled-Coil Peptide with a Reversible pH-Induced Oligomerization Switch.
Authors: Lizatovic, R. / Aurelius, O. / Stenstrom, O. / Drakenberg, T. / Akke, M. / Logan, D.T. / Andre, I.
History
DepositionOct 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pHiosYI
B: pHiosYI


Theoretical massNumber of molelcules
Total (without water)7,7062
Polymers7,7062
Non-polymers00
Water00
1
A: pHiosYI
B: pHiosYI

A: pHiosYI
B: pHiosYI

A: pHiosYI
B: pHiosYI


Theoretical massNumber of molelcules
Total (without water)23,1196
Polymers23,1196
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8220 Å2
ΔGint-81 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.068, 53.068, 136.114
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 28 / Label seq-ID: 1 - 28

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein/peptide pHiosYI


Mass: 3853.132 Da / Num. of mol.: 2 / Mutation: Y5(IYR) / Source method: obtained synthetically / Details: Designed sequence / Source: (synth.) synthetic construct (others)
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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 2 uL 10 mg/mL pHiosYI mixed with a 2 uL solution of the below components 0.1 M Na HEPES pH 7.5 0.2 M MgCl2 10% (v/v) PEG400 Al's oil was used to separate the external reservoir, which ...Details: 2 uL 10 mg/mL pHiosYI mixed with a 2 uL solution of the below components 0.1 M Na HEPES pH 7.5 0.2 M MgCl2 10% (v/v) PEG400 Al's oil was used to separate the external reservoir, which consisted of 15% (v/v) 2-propanol.
Temp details: The crystal was moved to 277 K during fishing and cryo-cooling.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.8 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 25, 2013
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 3.19→27.4 Å / Num. obs: 2301 / % possible obs: 95.6 % / Redundancy: 10.8 %
Details: Data quality statistics are with unmerged Friedel mates for data collection and merged Friedel mates for refinement
Rsym value: 0.05 / Net I/σ(I): 24.2
Reflection shellResolution: 3.2→3.4 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.6 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
MxCuBEdata collection
XDSdata reduction
AutoSol1.9_1692phasing
XDSdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 3.19→27.35 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.854 / SU B: 59.117 / SU ML: 0.835 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.951 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.4336 139 10.9 %RANDOM
Rwork0.3256 ---
obs0.3359 1131 93.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.25 Å2 / Biso mean: 120.615 Å2 / Biso min: 121.25 Å2
Baniso -1Baniso -2Baniso -3
1--3.78 Å2-1.89 Å2-0 Å2
2---3.78 Å2-0 Å2
3---12.27 Å2
Refinement stepCycle: final / Resolution: 3.19→27.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms464 0 0 0 464
Num. residues----56
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02476
X-RAY DIFFRACTIONr_bond_other_d0.0040.02477
X-RAY DIFFRACTIONr_angle_refined_deg1.532.09639
X-RAY DIFFRACTIONr_angle_other_deg1.12631106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.112554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.5627.27322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.4371598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.06152
X-RAY DIFFRACTIONr_chiral_restr0.0870.275
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02505
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0285
Refine LS restraints NCS

Ens-ID: 1 / Number: 2996 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.185→3.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.551 15 -
Rwork0.266 62 -
all-77 -
obs--79.38 %

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