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- PDB-6c51: Cross-alpha Amyloid-like Structure alphaAmL -

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Basic information

Entry
Database: PDB / ID: 6c51
TitleCross-alpha Amyloid-like Structure alphaAmL
ComponentsCross-alpha Amyloid-like Structure alphaAmL
KeywordsDE NOVO PROTEIN / Protein Design / Cross-alpha Amyloid
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsLiu, L. / Zhang, S.Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35GM122603 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
DepositionJan 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cross-alpha Amyloid-like Structure alphaAmL
C: Cross-alpha Amyloid-like Structure alphaAmL
B: Cross-alpha Amyloid-like Structure alphaAmL
D: Cross-alpha Amyloid-like Structure alphaAmL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,58711
Polymers11,8994
Non-polymers6887
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-81 kcal/mol
Surface area7580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.210, 53.210, 134.775
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11D-102-

PO4

21D-204-

HOH

31D-205-

HOH

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Components

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


Mass: 2974.649 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 45% MPD, 0.6 M NaH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11584 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11584 Å / Relative weight: 1
ReflectionResolution: 2→46.3 Å / Num. obs: 14468 / % possible obs: 99.9 % / Redundancy: 19.7 % / Net I/σ(I): 31.8
Reflection shellResolution: 2→2.05 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementResolution: 2→46.08 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.941 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.178 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26186 409 5 %RANDOM
Rwork0.2353 ---
obs0.23659 7841 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.599 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.23 Å2-0 Å2
2---0.45 Å20 Å2
3---1.47 Å2
Refinement stepCycle: 1 / Resolution: 2→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 38 15 865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.019861
X-RAY DIFFRACTIONr_bond_other_d0.0010.02942
X-RAY DIFFRACTIONr_angle_refined_deg0.9542.1241157
X-RAY DIFFRACTIONr_angle_other_deg0.76932170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.822599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.70121.48127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82415194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.392153
X-RAY DIFFRACTIONr_chiral_restr0.0410.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02840
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02139
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_it1.2114.094404
X-RAY DIFFRACTIONr_mcbond_other1.2124.088403
X-RAY DIFFRACTIONr_mcangle_it2.0826.082497
X-RAY DIFFRACTIONr_mcangle_other2.086.089498
X-RAY DIFFRACTIONr_scbond_it1.0934.681457
X-RAY DIFFRACTIONr_scbond_other1.0924.689458
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8136.998659
X-RAY DIFFRACTIONr_long_range_B_refined6.32174.1043052
X-RAY DIFFRACTIONr_long_range_B_other6.3274.1163053
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 23 -
Rwork0.275 571 -
obs--99.66 %
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)
13.614-0.17180.57085.9465-5.870913.50280.0789-0.0561-0.08050.0316-0.08590.03330.24260.18320.0070.014-0.00560.00990.0228-0.02360.03527.0201-20.8064-10.1939
25.64585.3684-0.999512.2273-3.09893.9662-0.0684-0.02320.07520.057-0.0047-0.1324-0.05240.0130.07310.04660.03480.01470.0756-0.01440.033236.6969-17.7437-18.779
32.32060.1968-0.66942.2596-0.58628.01410.0390.101-0.2092-0.1162-0.00230.19270.1644-0.1598-0.03670.0537-0.026-0.00340.0332-0.02760.14318.7071-24.5746-14.7086
47.57185.1244-0.13217.6487-0.34892.74340.03050.23210.0908-0.0795-0.00760.1940.0225-0.0793-0.02290.09550.06010.03490.06880.00020.042736.5994-21.6747-28.4739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 26
2X-RAY DIFFRACTION2B0 - 26
3X-RAY DIFFRACTION3C0 - 26
4X-RAY DIFFRACTION4D0 - 24

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