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- PDB-9dox: Fibrillar assembly of an L-enantiopure, C-alpha methylated, macro... -

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Basic information

Entry
Database: PDB / ID: 9dox
TitleFibrillar assembly of an L-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
ComponentsL-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 / SAD / Resolution: 2.25 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: L-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
a: L-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
B: L-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
b: L-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
C: L-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
c: L-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
D: L-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
d: L-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
E: L-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
e: L-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
F: L-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
f: L-enantiopure, C-alpha methylated, macrocyclic beta-hairpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,80018
Polymers17,44712
Non-polymers3,3536
Water46826
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 area8420 Å2
ΔGint-70 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.497, 57.497, 114.058
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
L-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.: 6 / Source method: obtained synthetically / Formula: C8H4I3NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.73 Å3/Da / Density % sol: 54.97 %
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) as a co-crystallant

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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: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 9732 / % possible obs: 99.9 % / Redundancy: 12.4 % / CC1/2: 0.977 / CC star: 0.994 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.035 / Rrim(I) all: 0.122 / Χ2: 1.663 / Net I/σ(I): 7.1 / Num. measured all: 120470
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.25-2.2912.30.4474800.9830.9960.1320.4660.677100
2.29-2.3312.90.4454670.9730.9930.1290.4640.746100
2.33-2.3813.40.3974590.9840.9960.1120.4130.77100
2.38-2.4213.10.354830.9890.9970.10.3640.849100
2.42-2.4813.50.3594680.9850.9960.1010.3730.818100
2.48-2.5313.20.3374710.9870.9970.0950.3510.823100
2.53-2.613.20.2884770.9890.9970.0820.2990.923100
2.6-2.6712.80.254710.9910.9980.0730.2611.027100
2.67-2.7512.50.2114840.9970.9990.0620.221.07100
2.75-2.83120.1884710.9940.9980.0560.1971.317100
2.83-2.9411.20.1514750.9940.9990.0470.1581.39999.6
2.94-3.0513.30.1434910.9950.9990.0420.1491.501100
3.05-3.1913.10.1244900.9940.9990.0360.1291.853100
3.19-3.36130.1134720.9980.9990.0330.1181.996100
3.36-3.5712.40.114920.9960.9990.0330.1152.225100
3.57-3.85120.0984900.9970.9990.030.1032.426100
3.85-4.2310.70.0924970.9970.9990.030.0972.872100
4.23-4.8512.20.0715050.99810.0220.0752.90199.8
4.85-6.111.80.0765190.99810.0240.083.594100
6.1-509.80.0755700.9980.9990.0250.0793.92399.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→40.69 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.136 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28393 489 5.1 %RANDOM
Rwork0.23699 ---
obs0.2393 9191 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.292 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.71 Å20 Å2
3---1.42 Å2
Refinement stepCycle: 1 / Resolution: 2.25→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 96 26 1334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131332
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161524
X-RAY DIFFRACTIONr_angle_refined_deg1.8822.0521836
X-RAY DIFFRACTIONr_angle_other_deg0.5821.8073546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6715144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33210300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021248
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02168
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_it2.5673.012624
X-RAY DIFFRACTIONr_mcbond_other2.5653.012624
X-RAY DIFFRACTIONr_mcangle_it3.9325.405768
X-RAY DIFFRACTIONr_mcangle_other3.935.404769
X-RAY DIFFRACTIONr_scbond_it3.8383.515708
X-RAY DIFFRACTIONr_scbond_other3.7583.488702
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7176.3311061
X-RAY DIFFRACTIONr_long_range_B_refined8.99735.891407
X-RAY DIFFRACTIONr_long_range_B_other8.86635.691401
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.302 Å
RfactorNum. reflection% reflection
Rfree0.294 34 -
Rwork0.209 641 -
obs--96.15 %

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