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- PDB-9gf4: CC-Hept-IV-hen2 variant peptide with Hendecad repeat substitution -

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Basic information

Entry
Database: PDB / ID: 9gf4
TitleCC-Hept-IV-hen2 variant peptide with Hendecad repeat substitution
ComponentsCC-Hept-IV-hen2
KeywordsDE NOVO PROTEIN / Hendecad Repeat / Coiled-Coil / De novo Design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsKurgan, K.W. / Martin, F.J.O. / Woolfson, D.N.
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
A: CC-Hept-IV-hen2
B: CC-Hept-IV-hen2
C: CC-Hept-IV-hen2
D: CC-Hept-IV-hen2
E: CC-Hept-IV-hen2
F: CC-Hept-IV-hen2
G: CC-Hept-IV-hen2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,40519
Polymers24,4387
Non-polymers96712
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16090 Å2
ΔGint-172 kcal/mol
Surface area10880 Å2
Unit cell
Length a, b, c (Å)38.546, 47.919, 153.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein/peptide
CC-Hept-IV-hen2


Mass: 3491.127 Da / Num. of mol.: 7 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5 M Ammonium sulfate, 0.1 M Sodium acetate 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.49→19.67 Å / Num. obs: 47155 / % possible obs: 99.8 % / Redundancy: 1 % / CC1/2: 0.9984 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.013 / Rrim(I) all: 0.047 / Net I/σ(I): 25.1
Reflection shellResolution: 1.49→1.52 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2201 / CC1/2: 0.9949 / Rpim(I) all: 0.102 / Rrim(I) all: 0.319 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→19.67 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.764 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1751 2435 5.2 %RANDOM
Rwork0.15067 ---
obs0.15195 44719 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.747 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å2-0 Å2-0 Å2
2---1.3 Å20 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.49→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 62 193 1973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121805
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161919
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.7822420
X-RAY DIFFRACTIONr_angle_other_deg0.5281.7554408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8755237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.33210321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02330
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_it3.0751.631975
X-RAY DIFFRACTIONr_mcbond_other3.0441.627973
X-RAY DIFFRACTIONr_mcangle_it4.2622.931211
X-RAY DIFFRACTIONr_mcangle_other4.2422.9271210
X-RAY DIFFRACTIONr_scbond_it5.7752.114830
X-RAY DIFFRACTIONr_scbond_other5.7722.119831
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3163.6311208
X-RAY DIFFRACTIONr_long_range_B_refined13.29318.922211
X-RAY DIFFRACTIONr_long_range_B_other13.25318.932211
X-RAY DIFFRACTIONr_rigid_bond_restr2.87733724
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.491→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 188 -
Rwork0.173 3137 -
obs--97.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.34970.0469-0.19430.5771-0.025610.761-0.02530.0161-0.01820.0146-0.03960.05960.024-0.44630.06490.0024-0.00290.00330.0217-0.00760.008-18.9768-5.556625.4568
20.60030.0899-1.4720.6589-0.890314.7881-0.01510.0534-0.0945-0.01060.002-0.01640.4367-0.16760.01310.0151-0.0029-0.00580.005-0.00750.0196-12.7711-11.442125.484
30.66640.0385-0.04530.72030.031416.1251-0.0115-0.00890.05760.0265-0.00590.0573-0.3914-0.37270.01740.01080.00910.00060.0088-0.00160.0091-18.353.05726.5526
40.6286-0.15740.50511.0081-1.484414.6990.0280.01820.03770.0694-0.0395-0.134-0.27160.5410.01150.0164-0.0172-0.00740.03050.00090.022-2.87885.267726.8086
50.8392-0.20050.96450.5712-1.360816.164-0.034800.10930.0712-0.0397-0.0485-0.62530.22040.07450.025-0.0096-0.00370.00440.00060.016-11.09887.826526.7684
60.93230.1647-1.14020.8669-1.702515.2318-0.0634-0.0189-0.1381-0.037-0.0568-0.15140.50360.2540.12020.0180.00750.00390.00540.00750.0466-4.1033-10.07725.3014
70.38780.158-0.52740.9263-1.887913.4403-0.003-0.0102-0.04030.005-0.0707-0.1690.13470.49110.07370.0034-0.0002-0.00570.03980.00570.03980.0946-2.581325.6114
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 35
2X-RAY DIFFRACTION2B0 - 35
3X-RAY DIFFRACTION3C0 - 35
4X-RAY DIFFRACTION4D0 - 35
5X-RAY DIFFRACTION5E0 - 35
6X-RAY DIFFRACTION6F0 - 35
7X-RAY DIFFRACTION7G0 - 35

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