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- PDB-4nw9: Crystal structure of macrocycles containing Abeta17-23 (LVF(MEA)A... -

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Basic information

Entry
Database: PDB / ID: 4nw9
TitleCrystal structure of macrocycles containing Abeta17-23 (LVF(MEA)AED) and Abeta30-36 (AIIGL(ORN)V)
ComponentsCyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
Keywordsde novo protein / protein binding / beta-sheet / beta-hairpin / amyloid
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsSpencer, R.K. / Li, H. / Nowick, J.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: X-ray crystallographic structures of trimers and higher-order oligomeric assemblies of a peptide derived from A beta (17-36).
Authors: Spencer, R.K. / Li, H. / Nowick, J.S.
History
DepositionDec 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Jul 9, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
B: Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
C: Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
D: Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
E: Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
F: Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
G: Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
H: Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
I: Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
J: Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
K: Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
L: Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,31017
Polymers21,15812
Non-polymers1525
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.220, 68.220, 92.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-108-

HOH

21H-125-

HOH

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Components

#1: Protein/peptide
Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V


Mass: 1763.129 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 0.1 M HEPES, 24% Jeffamine M-600, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2013
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.654→36.54 Å / Num. obs: 29970 / % possible obs: 98.4 % / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 31.33 Å2 / Rmerge(I) obs: 0.05206 / Net I/σ(I): 13.78
Reflection shellResolution: 1.65→1.7 Å / % possible all: 87.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NW8

4nw8


Resolution: 1.66→36.54 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.89 / Stereochemistry target values: MLHL / Details: TLS PARAMETERS WERE USED FOR EACH MACROCYCLE
RfactorNum. reflection% reflection
Rfree0.209 1505 5.04 %
Rwork0.189 --
obs0.19 26597 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→36.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 5 247 1740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111512
X-RAY DIFFRACTIONf_angle_d1.592004
X-RAY DIFFRACTIONf_dihedral_angle_d34.546696
X-RAY DIFFRACTIONf_chiral_restr0.086252
X-RAY DIFFRACTIONf_plane_restr0.007240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6553-1.70880.37091180.33222211X-RAY DIFFRACTION85
1.7088-1.76980.27541350.25792578X-RAY DIFFRACTION100
1.7698-1.84070.25081380.2342581X-RAY DIFFRACTION100
1.8407-1.92450.26491340.22832585X-RAY DIFFRACTION100
1.9245-2.02590.27471420.20972617X-RAY DIFFRACTION100
2.0259-2.15280.24941350.19192593X-RAY DIFFRACTION100
2.1528-2.3190.24581360.19422616X-RAY DIFFRACTION100
2.319-2.55230.21861370.19872613X-RAY DIFFRACTION100
2.5523-2.92150.23141410.19972633X-RAY DIFFRACTION100
2.9215-3.68030.1961380.17922663X-RAY DIFFRACTION100
3.6803-36.54630.1791510.17022676X-RAY DIFFRACTION96
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)
10.84620.8178-0.69341.2916-0.06281.3031-0.376-0.51950.08390.52550.08190.48210.0699-0.4702-0.00020.32470.0180.02750.3551-0.05990.454515.0938-9.057913.2719
21.5916-0.74911.16090.6511-0.18221.3017-0.09830.11480.7223-0.38860.09820.94760.1165-0.0881-0.00020.3671-0.0081-0.02430.3389-0.04280.468811.3764-7.59461.8722
31.29220.9723-0.33552.0909-1.10480.6881-0.0194-0.168-0.8996-0.05030.1804-0.14030.1762-0.34650.04820.2851-0.0389-0.02790.3746-0.0390.297123.1128-9.01834.1148
42.3041-1.0769-0.72970.59470.03831.34460.1623-0.5821-0.38370.8672-0.36510.5671-0.19050.8426-0.00090.3863-0.06090.06570.552-0.02280.39776.9191-24.694718.211
51.34280.31530.59450.31980.49221.10590.1679-0.13170.9755-0.0678-0.29750.019-0.9534-0.5882-0.00850.33510.0440.05760.3695-0.06240.40610.3575-21.12968.6735
61.97730.16640.17671.4771-1.37451.33430.17250.995-0.5522-0.50080.01360.17790.29970.16290.00950.2972-0.00870.0410.3444-0.02430.31854.8394-32.40899.1917
71.14990.55160.10360.5709-0.5971.5283-0.0981-0.34970.1177-0.0712-0.08520.49540.0235-0.2137-0.00010.3378-0.048-0.00950.3948-0.01490.34318.7347-23.1188-7.8228
80.9314-0.29760.03052.01451.66661.4649-0.01270.11540.06290.0228-0.18540.0024-0.36080.2833-0.00030.338-0.058-0.01720.39580.00220.307420.7866-21.7476-8.6803
91.1507-0.24631.13842.54631.4072.218-0.1109-0.2625-0.09290.1650.0572-0.33310.2820.288800.2646-0.01560.02920.27670.00280.282716.1819-32.3617-5.3791
101.1141-0.0583-0.42921.2348-0.05580.39220.1213-0.0893-0.14740.18220.32530.45720.7273-0.4158-0.00070.397-0.01460.00080.36010.05490.337823.318-34.107811.7902
112.65081.15550.43150.8681-0.09720.33260.12880.6557-0.0855-0.4644-0.0353-0.7426-0.08690.03020.00040.36420.0242-0.02650.348-0.03970.351430.541-26.07946.4835
122.78940.31790.2091.0456-0.97561.391-0.0808-0.74420.90890.3049-0.0250.0756-0.3640.17850.02250.34310.0297-0.02580.32750.02380.354225.5873-23.580817.1996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 16 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 16 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 16 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 16 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 16 )
7X-RAY DIFFRACTION7chain 'G' and (resid 1 through 16 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 16 )
9X-RAY DIFFRACTION9chain 'I' and (resid 1 through 16 )
10X-RAY DIFFRACTION10chain 'J' and (resid 1 through 16 )
11X-RAY DIFFRACTION11chain 'K' and (resid 1 through 16 )
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 16 )

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