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- PDB-9doy: Fibrillar assembly of an D-enantiopure, C-alpha methylated, macro... -

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Basic information

Entry
Database: PDB / ID: 9doy
TitleFibrillar assembly of an D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
ComponentsD-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
KeywordsPROTEIN FIBRIL / MAX1 / fibril / hydrogel / C-alpha methylated macrocyclic beta-hairpin
Function / homologyChem-I3C
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsSamdin, T.D. / Lubkowski, J. / Anderson, C.F. / Schneider, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1ZIABC011313-14 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: From Hydrogel to Crystal: A Molecular Design Strategy that Chemically Modifies Racemic Gel-Forming Peptides to Furnish Crystalline Fibrils Stabilized by Parallel Rippled beta-Sheets.
Authors: Samdin, T.D. / Lubkowski, J. / Anderson, C.F. / Schneider, J.P.
History
DepositionSep 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
a: D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
B: D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
b: D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
C: D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
c: D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
D: D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
d: D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
E: D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
e: D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
F: D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
f: D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,35919
Polymers17,44712
Non-polymers3,9127
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, TEM experiments of a homologous macrocyclic beta-hairpin peptide without the C-alpha methyl group show evidence of self-assembly and fibrillization, correlating with ...Evidence: electron microscopy, TEM experiments of a homologous macrocyclic beta-hairpin peptide without the C-alpha methyl group show evidence of self-assembly and fibrillization, correlating with the deposited X-ray crystallographic structure.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-71 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.475, 57.475, 113.575
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein/peptide
D-enantiopure, C-alpha methylated, macrocyclic beta-hairpin


Mass: 1453.895 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H4I3NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.4-0.6 M sodium potassium phosphate, pH 7.0, 26% v/v PEG400, 2-12 mM I3C (5-amino-2,4,6-triiodoisphthalic acid)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 15438 / % possible obs: 99.3 % / Redundancy: 19.2 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.045 / Rrim(I) all: 0.174 / Χ2: 2.459 / Net I/σ(I): 39.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.92-1.9518.90.6436930.9210.9790.1490.6620.93892
1.95-1.9922.80.5917640.9660.9910.1270.6051.113100
1.99-2.0322.80.5327410.9710.9930.1150.5451.18499.9
2.03-2.0722.90.4937680.9750.9940.1060.5051.271100
2.07-2.1122.50.4537470.9670.9910.10.4641.422100
2.11-2.1622.60.4467750.9720.9930.0980.4571.43899.9
2.16-2.2221.90.3927480.9820.9950.0880.4021.547100
2.22-2.2821.40.3617590.970.9920.0820.3711.59100
2.28-2.3420.60.3327680.9610.990.0780.3421.70899.9
2.34-2.4218.40.3057640.9640.9910.0780.3161.906100
2.42-2.5119.50.2817720.9720.9930.070.291.9299.9
2.51-2.6121.10.2587610.9840.9960.0610.2662.09100
2.61-2.7220.10.2247700.9830.9960.0560.2322.47899.9
2.72-2.8718.90.1947720.9830.9960.050.2012.71199.9
2.87-3.0517.30.1667830.9840.9960.0470.1733.23399.4
3.05-3.2815.60.1447640.9870.9970.0440.1523.64599.2
3.28-3.61140.1317840.9890.9970.0430.1394.67398.5
3.61-4.1415.90.1168000.9940.9980.0350.1214.75899.5
4.14-5.2114.40.1038070.990.9970.0340.1095.81799
5.21-5014.90.0898980.99910.0260.0947.45299.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→40.43 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.888 / SU B: 3.483 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29613 692 4.8 %RANDOM
Rwork0.24556 ---
obs0.24791 13671 93.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.035 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.78 Å2
Refinement stepCycle: 1 / Resolution: 1.92→40.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 112 39 1363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131367
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161589
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.851893
X-RAY DIFFRACTIONr_angle_other_deg0.4531.6343688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8515152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43110304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021298
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02176
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_it2.452.509631
X-RAY DIFFRACTIONr_mcbond_other2.4482.508632
X-RAY DIFFRACTIONr_mcangle_it3.5894.486778
X-RAY DIFFRACTIONr_mcangle_other3.594.485779
X-RAY DIFFRACTIONr_scbond_it3.623.013736
X-RAY DIFFRACTIONr_scbond_other3.5772.998730
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4075.3821104
X-RAY DIFFRACTIONr_long_range_B_refined8.21831.651519
X-RAY DIFFRACTIONr_long_range_B_other8.15531.311513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.966 Å
RfactorNum. reflection% reflection
Rfree0.285 54 -
Rwork0.208 996 -
obs--95.89 %

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