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- PDB-6o3n: Cross-alpha Amyloid-like Structure alphaAmA -

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Basic information

Entry
Database: PDB / ID: 6o3n
TitleCross-alpha Amyloid-like Structure alphaAmA
ComponentsCross-alpha Amyloid-like Structure alphaAmA
KeywordsDE NOVO PROTEIN / alpha-amyloid / De Novo Design / coiled-coil / fibril
Biological speciessynthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsZhang, S.-Q. / Liu, L. / DeGrado, W.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122603 United States
National Science Foundation (NSF, United States)CHE1413295 United States
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Designed peptides that assemble into cross-alpha amyloid-like structures
Authors: Zhang, S.Q. / Huang, H. / Yang, J. / Kratochvil, H.T. / Lolicato, M. / Liu, Y. / Shu, X. / Liu, L. / DeGrado, W.F.
History
DepositionFeb 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cross-alpha Amyloid-like Structure alphaAmA
B: Cross-alpha Amyloid-like Structure alphaAmA
C: Cross-alpha Amyloid-like Structure alphaAmA
D: Cross-alpha Amyloid-like Structure alphaAmA
E: Cross-alpha Amyloid-like Structure alphaAmA
F: Cross-alpha Amyloid-like Structure alphaAmA
G: Cross-alpha Amyloid-like Structure alphaAmA
H: Cross-alpha Amyloid-like Structure alphaAmA
I: Cross-alpha Amyloid-like Structure alphaAmA
J: Cross-alpha Amyloid-like Structure alphaAmA
K: Cross-alpha Amyloid-like Structure alphaAmA
L: Cross-alpha Amyloid-like Structure alphaAmA
M: Cross-alpha Amyloid-like Structure alphaAmA
N: Cross-alpha Amyloid-like Structure alphaAmA
O: Cross-alpha Amyloid-like Structure alphaAmA
P: Cross-alpha Amyloid-like Structure alphaAmA


Theoretical massNumber of molelcules
Total (without water)46,92116
Polymers46,92116
Non-polymers00
Water00
1
A: Cross-alpha Amyloid-like Structure alphaAmA
B: Cross-alpha Amyloid-like Structure alphaAmA
C: Cross-alpha Amyloid-like Structure alphaAmA
D: Cross-alpha Amyloid-like Structure alphaAmA
E: Cross-alpha Amyloid-like Structure alphaAmA
F: Cross-alpha Amyloid-like Structure alphaAmA
G: Cross-alpha Amyloid-like Structure alphaAmA
H: Cross-alpha Amyloid-like Structure alphaAmA
I: Cross-alpha Amyloid-like Structure alphaAmA
J: Cross-alpha Amyloid-like Structure alphaAmA
K: Cross-alpha Amyloid-like Structure alphaAmA
L: Cross-alpha Amyloid-like Structure alphaAmA
M: Cross-alpha Amyloid-like Structure alphaAmA
N: Cross-alpha Amyloid-like Structure alphaAmA
O: Cross-alpha Amyloid-like Structure alphaAmA
P: Cross-alpha Amyloid-like Structure alphaAmA

A: Cross-alpha Amyloid-like Structure alphaAmA
B: Cross-alpha Amyloid-like Structure alphaAmA
C: Cross-alpha Amyloid-like Structure alphaAmA
D: Cross-alpha Amyloid-like Structure alphaAmA
E: Cross-alpha Amyloid-like Structure alphaAmA
F: Cross-alpha Amyloid-like Structure alphaAmA
G: Cross-alpha Amyloid-like Structure alphaAmA
H: Cross-alpha Amyloid-like Structure alphaAmA
I: Cross-alpha Amyloid-like Structure alphaAmA
J: Cross-alpha Amyloid-like Structure alphaAmA
K: Cross-alpha Amyloid-like Structure alphaAmA
L: Cross-alpha Amyloid-like Structure alphaAmA
M: Cross-alpha Amyloid-like Structure alphaAmA
N: Cross-alpha Amyloid-like Structure alphaAmA
O: Cross-alpha Amyloid-like Structure alphaAmA
P: Cross-alpha Amyloid-like Structure alphaAmA


Theoretical massNumber of molelcules
Total (without water)93,84232
Polymers93,84232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area39420 Å2
ΔGint-588 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.816, 164.816, 164.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein/peptide
Cross-alpha Amyloid-like Structure alphaAmA


Mass: 2932.569 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
Has protein modificationN

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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: 5.94 Å3/Da / Density % sol: 79.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 45% MPD, 0.25M NaH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.335
11L, -K, H20.317
11-H, L, K30.348
ReflectionResolution: 3.7→116.5 Å / Num. obs: 12514 / % possible obs: 99.7 % / Redundancy: 25.6 % / CC1/2: 0.997 / Rrim(I) all: 0.098 / Net I/σ(I): 18.48
Reflection shellResolution: 3.7→3.93 Å / Redundancy: 25.5 % / Mean I/σ(I) obs: 1.59 / Num. unique obs: 1946 / CC1/2: 0.465 / Rrim(I) all: 2.11 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSVERSION Jan 26, 2018 BUILT=20180409data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C4Z

6c4z


Resolution: 3.7→116.5 Å / Cor.coef. Fo:Fc: 0.852 / Cor.coef. Fo:Fc free: 0.868 / SU B: 26.952 / SU ML: 0.436 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.117 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31925 1189 9.6 %RANDOM
Rwork0.29697 ---
obs0.29888 11175 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 83.036 Å2
Baniso -1Baniso -2Baniso -3
1--8.98 Å2-0 Å2-0 Å2
2---8.98 Å2-0 Å2
3---17.95 Å2
Refinement stepCycle: 1 / Resolution: 3.7→116.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 0 0 2352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132336
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172432
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.5883216
X-RAY DIFFRACTIONr_angle_other_deg1.2611.5745344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9375368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.11215288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0560.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022576
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02368
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.688→3.783 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 79 -
Rwork0.321 718 -
obs--89.05 %

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