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- PDB-4ntr: Crystal structure of macrocycles containing Abeta 17-23 (LVFFAED)... -

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Basic information

Entry
Database: PDB / ID: 4ntr
TitleCrystal structure of macrocycles containing Abeta 17-23 (LVFFAED) and Abeta 30-36 (AII(SAR)L(ORN)V)
ComponentsCyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
Keywordsde novo protein / protein binding / beta-sheet / beta-hairpin / amyloid / amyloid beta-sheet mimic / de novo protein-protein binding complex
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 2, 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 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / 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)LVFFAED(ORN)AII(SAR)L(ORN)V
B: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
C: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
D: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
E: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
F: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
G: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
H: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
I: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
J: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
K: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
L: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
M: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
N: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
O: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
P: Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,56327
Polymers28,21016
Non-polymers35311
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.000, 68.000, 169.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein/peptide
Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V


Mass: 1763.128 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 298 K / pH: 6.75
Details: 0.1 M HEPES, pH 6.75, 31% Jeffamine-M600, 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: 1.7→34.36 Å / Num. obs: 31708 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 24.24 Å2 / Rmerge(I) obs: 0.04665 / Net I/σ(I): 12.63
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 2 / % possible all: 92.8

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Processing

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

4ntp


Resolution: 1.7→34.36 Å
Isotropic thermal model: Isotropic with TLS parameters for each macrocycle.
σ(F): 1.99 / Phase error: 24.85 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.226 1966 6.2 %
Rwork0.2 --
obs0.202 31685 98.7 %
all-31708 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→34.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 11 244 2239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062016
X-RAY DIFFRACTIONf_angle_d1.1632688
X-RAY DIFFRACTIONf_dihedral_angle_d33.043960
X-RAY DIFFRACTIONf_chiral_restr0.043336
X-RAY DIFFRACTIONf_plane_restr0.006320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7003-1.74280.30111250.26741999X-RAY DIFFRACTION93
1.7428-1.78990.32311440.24352173X-RAY DIFFRACTION100
1.7899-1.84260.30031370.23832129X-RAY DIFFRACTION100
1.8426-1.90210.26431420.22462153X-RAY DIFFRACTION100
1.9021-1.970.25951500.21292120X-RAY DIFFRACTION100
1.97-2.04890.21331520.18992148X-RAY DIFFRACTION100
2.0489-2.14210.19491370.19082160X-RAY DIFFRACTION100
2.1421-2.25510.21271340.19192133X-RAY DIFFRACTION100
2.2551-2.39630.24361570.20242124X-RAY DIFFRACTION100
2.3963-2.58130.25141460.21262118X-RAY DIFFRACTION99
2.5813-2.84090.26761410.21372160X-RAY DIFFRACTION99
2.8409-3.25180.24811270.19642119X-RAY DIFFRACTION98
3.2518-4.09580.21941270.18882122X-RAY DIFFRACTION98
4.0958-34.37070.17881470.19042061X-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)
17.63494.1301-0.29838.5214-4.43454.5230.3120.30330.4580.21150.32140.47840.2715-0.9498-0.76110.27480.0162-0.02790.1560.04050.3217-6.57664.8543-4.5935
26.47634.58655.21149.62976.77049.4470.01140.605-0.0464-0.10260.0756-0.5332-0.33350.7441-0.05030.2915-0.0327-0.07310.1890.03360.29185.430364.0535-7.2718
34.5802-5.44313.05148.2474-3.49344.9995-0.8652-0.32370.1191.30420.4286-0.2288-0.70210.52130.47120.43-0.0269-0.0820.26340.040.35121.79267.8813.7616
46.5227-0.99895.7225.6602-1.19124.9637-0.0676-0.293-0.09150.23890.10460.2733-0.3492-0.5356-0.13560.28120.0272-0.03390.18930.00320.2258-7.01852.71794.385
53.62963.5585-0.38424.2526-1.41418.2174-0.3471-0.0025-0.058-0.21920.0168-0.2941-0.10650.49560.42370.26560.0396-0.02790.1540.01510.28311.680849.7905-3.5319
64.0107-2.2755-4.60829.17113.92928.0458-0.3307-0.51660.61380.90280.3205-0.3646-0.14020.4722-0.04410.3078-0.0098-0.10610.1904-0.01970.23454.770953.89197.3537
76.5084-0.34743.01064.54244.47826.2504-0.0110.13920.1233-0.3765-0.0298-0.2551-1.1163-0.0476-0.02480.26630.0469-0.00170.1926-0.0140.2271-8.149752.0655-25.7071
88.25266.19975.0654.71163.85598.5596-0.2157-0.66650.5554-0.2434-0.38020.363-0.0665-0.46130.6350.20510.0773-0.01430.2056-0.02870.2934-7.64845.5493-19.0952
95.5174.6765-1.36854.93-0.27433.6405-0.2832-1.253-1.4013-0.5961-0.3193-0.0540.864-0.18330.79420.3880.01220.01840.3139-0.01480.4091-12.521940.2965-16.2879
107.7492-3.42172.61695.7381-5.04145.28740.37990.6073-0.015-0.7763-0.37940.93790.5855-0.2529-0.05090.23730.063-0.04660.2831-0.04370.2475-15.081942.4431-28.6399
115.55050.4114-2.18857.9594-5.98465.51450.3716-0.31280.35570.14550.12420.22650.0071.0621-0.24250.15290.0628-0.01750.2619-0.04840.261-20.504655.6652-14.1672
124.10060.3522-0.70344.2666-4.76258.34591.28060.16311.33150.08480.29030.3003-1.44390.9137-0.96970.3630.08320.07950.3811-0.00350.4199-17.0760.1442-19.5364
137.23371.3895-1.22463.14340.63518.14650.44240.3185-0.0839-0.7842-0.82120.15850.115-0.69150.35790.23110.0788-0.00960.391-0.09280.2823-25.665452.0182-25.0519
145.4005-1.48576.8784.5617-0.27079.1675-0.0655-0.2885-0.23470.3614-0.02070.36060.2641-0.50860.06810.21930.02530.0120.307-0.08630.2736-24.188146.9621-14.0176
159.0505-5.06472.71153.8005-2.06028.02850.40240.4283-0.51120.0497-0.62160.564-0.6043-0.43120.01680.3146-0.04160.02550.2124-0.00140.2388-5.731376.9757-19.8511
165.1707-4.2515-5.43744.41154.9776.26530.03060.3784-0.81871.0788-0.46210.3530.6324-0.33030.26690.40610.012-0.01990.31350.0050.3621-4.248969.6691-22.169
173.33462.32810.13927.2599-2.9947.9157-0.626-0.258-0.2041-0.25820.33090.21731.0169-0.42260.26110.3461-0.01960.03910.2917-0.00710.1764-1.478871.5941-35.56
183.16513.4112-2.7747.8108-0.95167.8835-0.40860.2876-0.1966-0.26080.34950.3290.3615-0.09460.16840.2486-0.0142-0.0290.2638-0.02180.1743-35.807552.0337-0.3838
192.581.3015-1.57542.95031.57497.011-0.270.5945-0.33230.2263-0.35290.28360.4963-0.99050.43390.2827-0.01080.0180.3025-0.0280.172-39.827857.57515.3812
205.1003-5.1085-5.06755.53495.31435.6187-0.25250.5222-0.26451.1022-0.14830.3221.3114-0.07920.27540.49240.01940.00340.3807-0.04290.2589-38.603350.2913.0019
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 8 )
9X-RAY DIFFRACTION9chain 'H' and (resid 9 through 16 )
10X-RAY DIFFRACTION10chain 'I' and (resid 1 through 16 )
11X-RAY DIFFRACTION11chain 'J' and (resid 1 through 8 )
12X-RAY DIFFRACTION12chain 'J' and (resid 9 through 16 )
13X-RAY DIFFRACTION13chain 'K' and (resid 1 through 16 )
14X-RAY DIFFRACTION14chain 'L' and (resid 1 through 16 )
15X-RAY DIFFRACTION15chain 'M' and (resid 1 through 8 )
16X-RAY DIFFRACTION16chain 'M' and (resid 9 through 16 )
17X-RAY DIFFRACTION17chain 'N' and (resid 1 through 16 )
18X-RAY DIFFRACTION18chain 'O' and (resid 1 through 16 )
19X-RAY DIFFRACTION19chain 'P' and (resid 1 through 8 )
20X-RAY DIFFRACTION20chain 'P' and (resid 9 through 16 )

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