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- PDB-9gf3: CC-Hept-hen2 variant peptide with Hendecad repeat substitution -

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Basic information

Entry
Database: PDB / ID: 9gf3
TitleCC-Hept-hen2 variant peptide with Hendecad repeat substitution
ComponentsCC-Hept-hen2
KeywordsDE NOVO PROTEIN / Hendecad Repeat / Coiled-Coil / De novo Design
Function / homologyFORMIC ACID / AMMONIUM ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.65 Å
AuthorsKurgan, K.W. / Martin, F.J.O.
Funding support United States, United Kingdom, 7items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)BB/V004220/1 United States
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V004220/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00661X/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/G036764 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Royal SocietyWM140008 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S002820/1 United Kingdom
CitationJournal: Chem Sci / Year: 2025
Title: Exchange, promiscuity, and orthogonality in de novo designed coiled-coil peptide assemblies.
Authors: Kurgan, K.W. / Martin, F.J.O. / Dawson, W.M. / Brunnock, T. / Orr-Ewing, A.J. / Woolfson, D.N.
History
DepositionAug 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: CC-Hept-hen2
N: CC-Hept-hen2
C: CC-Hept-hen2
D: CC-Hept-hen2
E: CC-Hept-hen2
F: CC-Hept-hen2
G: CC-Hept-hen2
H: CC-Hept-hen2
I: CC-Hept-hen2
J: CC-Hept-hen2
K: CC-Hept-hen2
L: CC-Hept-hen2
A: CC-Hept-hen2
B: CC-Hept-hen2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,10838
Polymers49,26914
Non-polymers1,84024
Water7,188399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.267, 61.754, 154.441
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 14 molecules MNCDEFGHIJKLAB

#1: Protein/peptide
CC-Hept-hen2


Mass: 3519.183 Da / Num. of mol.: 14 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 423 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium formate dihydrate, 20%w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→57.41 Å / Num. obs: 70317 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 1 / Rmerge(I) obs: 0.02 / Rpim(I) all: 0.02 / Rrim(I) all: 0.028 / Net I/σ(I): 19
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3458 / CC1/2: 0.911 / Rpim(I) all: 0.229 / Rrim(I) all: 0.324 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.65→57.41 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.003 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19963 3460 4.9 %RANDOM
Rwork0.17668 ---
obs0.17786 66776 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.211 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å2-0 Å2-0 Å2
2---0.06 Å2-0 Å2
3----2.2 Å2
Refinement stepCycle: 1 / Resolution: 1.65→57.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 119 399 3989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123649
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163943
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.8174861
X-RAY DIFFRACTIONr_angle_other_deg0.5821.7669080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0785480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08910702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024136
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02666
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5042.2941946
X-RAY DIFFRACTIONr_mcbond_other2.5062.2961947
X-RAY DIFFRACTIONr_mcangle_it3.6944.0812415
X-RAY DIFFRACTIONr_mcangle_other3.6764.0772414
X-RAY DIFFRACTIONr_scbond_it5.1973.1311703
X-RAY DIFFRACTIONr_scbond_other5.1963.1321704
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0865.2342438
X-RAY DIFFRACTIONr_long_range_B_refined9.67636.564505
X-RAY DIFFRACTIONr_long_range_B_other9.57835.254386
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 238 -
Rwork0.29 4924 -
obs--100 %

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