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- PDB-9dp0: Fibrillar assembly of racemic, C-alpha methylated, macrocyclic be... -

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Basic information

Entry
Database: PDB / ID: 9dp0
TitleFibrillar assembly of racemic, C-alpha methylated, macrocyclic beta-hairpins
Componentsracemic, C-alpha methylated, macrocyclic beta-hairpin
KeywordsPROTEIN FIBRIL / MAX1 / fibril / hydrogel / C-alpha methylated macrocyclic beta-hairpin
Function / homologyCITRATE ANION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: racemic, C-alpha methylated, macrocyclic beta-hairpin
B: racemic, C-alpha methylated, macrocyclic beta-hairpin
C: racemic, C-alpha methylated, macrocyclic beta-hairpin
D: racemic, C-alpha methylated, macrocyclic beta-hairpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2436
Polymers5,8164
Non-polymers4272
Water30617
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 area2870 Å2
ΔGint-23 kcal/mol
Surface area3610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.267, 32.657, 36.565
Angle α, β, γ (deg.)76.04, 70.87, 65.18
Int Tables number2
Space group name H-MP-1

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Components

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


Mass: 1453.895 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium tartrate dibasic, pH 6.0-6.3, 26-36% v/v PEG MME

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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: Mar 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→29.42 Å / Num. obs: 6796 / % possible obs: 90.4 % / Redundancy: 4.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.099 / Rrim(I) all: 0.132 / Net I/σ(I): 16.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
5.42-29.430.0643280.9950.0420.07789.13
4.31-5.420.06783590.9970.040.07993.01
3.76-4.310.1063730.9870.0610.122
3.42-3.760.112980.9920.0640.127
3.17-3.420.1183250.9870.0670.136
2.99-3.170.1253420.9870.0710.143
2.84-2.990.1453440.9910.0810.167
2.71-2.840.1373570.9910.0750.156
2.61-2.710.1793530.9810.1010.205
2.52-2.610.1723580.980.0950.197
2.44-2.520.1732960.9750.0960.198
2.37-2.440.1622990.980.090.185
2.31-2.370.1793570.9770.0990.205
2.25-2.310.1923360.9850.1080.221
2.2-2.250.1883360.9870.1030.215
2.15-2.20.1943530.9880.1080.222
2.11-2.150.2323580.9640.130.266
2.07-2.110.2223310.9730.1240.254
2.03-2.070.2513380.9270.1420.289
2-2.030.2513550.9620.1420.289
2-29.420.11467960.9960.0660.132

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.42 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.476 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27188 339 5 %RANDOM
Rwork0.24705 ---
obs0.24839 6456 90.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.829 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20.03 Å21.08 Å2
2--0.48 Å20.03 Å2
3----0.84 Å2
Refinement stepCycle: 1 / Resolution: 2→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms404 0 29 17 450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.013439
X-RAY DIFFRACTIONr_bond_other_d0.0060.016532
X-RAY DIFFRACTIONr_angle_refined_deg2.3911.955595
X-RAY DIFFRACTIONr_angle_other_deg1.1541.7871248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.273548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51110100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1350.281
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02384
X-RAY DIFFRACTIONr_gen_planes_other0.0050.0248
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_it2.3131.618208
X-RAY DIFFRACTIONr_mcbond_other2.321.614207
X-RAY DIFFRACTIONr_mcangle_it3.312.882256
X-RAY DIFFRACTIONr_mcangle_other3.3042.883257
X-RAY DIFFRACTIONr_scbond_it8.3923.301231
X-RAY DIFFRACTIONr_scbond_other8.3623.284230
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.135.114340
X-RAY DIFFRACTIONr_long_range_B_refined13.59924.751365
X-RAY DIFFRACTIONr_long_range_B_other13.59424.781366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 21 -
Rwork0.27 489 -
obs--92.9 %

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