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- PDB-6cg4: Covalently crosslinked trimer of a macrocyclic peptide derived fr... -

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Basic information

Entry
Database: PDB / ID: 6cg4
TitleCovalently crosslinked trimer of a macrocyclic peptide derived from Abeta(17-36) - (ORN)LCVFFCED(ORN)AII(2-nitrobenzylglycine)L(ORN)V
ComponentsORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-EZY-LEU-ORN-VAL
KeywordsNEUROPEPTIDE / Amyloid / oligomer / Alzheimer's Disease / Abeta
Function / homologyIODIDE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2.083 Å
AuthorsSalveson, P.J. / Nowick, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097562 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Controlling the Oligomerization State of A beta-Derived Peptides with Light.
Authors: Salveson, P.J. / Haerianardakani, S. / Thuy-Boun, A. / Kreutzer, A.G. / Nowick, J.S.
History
DepositionFeb 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: 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: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-EZY-LEU-ORN-VAL
B: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-EZY-LEU-ORN-VAL
C: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-EZY-LEU-ORN-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,10614
Polymers5,7193
Non-polymers1,38711
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-23 kcal/mol
Surface area4170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.317, 39.317, 59.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-102-

IOD

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Components

#1: Protein/peptide ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-EZY-LEU-ORN-VAL


Mass: 1906.272 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#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.: 21 / 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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 4.5 0.2 M sodium chloride 28% 2-methyl-2,4-pentanediol 0.1 M potassium iodide

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Dec 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.03→32.8 Å / Num. obs: 5269 / % possible obs: 100 % / Redundancy: 28.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Net I/σ(I): 33.1
Reflection shellResolution: 2.03→2.08 Å / Rmerge(I) obs: 0.241 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.083→32.783 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.61
RfactorNum. reflection% reflection
Rfree0.263 268 9.74 %
Rwork0.2051 --
obs0.2105 5269 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.083→32.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms396 10 8 21 435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005421
X-RAY DIFFRACTIONf_angle_d0.915563
X-RAY DIFFRACTIONf_dihedral_angle_d26.122282
X-RAY DIFFRACTIONf_chiral_restr0.11563
X-RAY DIFFRACTIONf_plane_restr0.00267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0832-2.29280.31171320.22291170X-RAY DIFFRACTION98
2.2928-2.62440.31521370.22981165X-RAY DIFFRACTION98
2.6244-3.3060.26161150.21091221X-RAY DIFFRACTION100
3.306-32.7870.22771290.18641200X-RAY DIFFRACTION100
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)
10.13060.05250.12030.3440.07710.2640.02060.0089-0.0098-0.0295-0.11530.07730.05790.0174-0.67560.1395-0.0170.03040.1368-0.04810.054126.3181-13.5325-17.9916
24.57041.59570.84532.61271.03434.4121-0.08490.20440.379-0.12110.03680.1451-0.4498-0.22120.12410.2797-0.0134-0.06020.16450.03150.149719.9321-5.1678-27.4955
30.1473-0.52680.59032.6221-2.98083.39590.21180.11690.1156-0.11310.04990.5659-0.0076-0.0628-0.18480.15650.03590.0030.15210.02340.219612.2778-12.4634-18.1216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:16 )A1 - 16
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:16 )B1 - 16
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:16 )C1 - 16

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