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- PDB-5hpp: Crystal structure of a macrocyclic beta-sheet peptide derived fro... -

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Basic information

Entry
Database: PDB / ID: 5hpp
TitleCrystal structure of a macrocyclic beta-sheet peptide derived from transthyretin (106-121) - (ORN)TIA(MAA)LLS(ORN)S(PHI)STTAV
ComponentsORN-THR-ILE-ALA-MAA-LEU-LEU-SER-ORN-SER-PHI-SER-THR-THR-ALA-VAL
KeywordsDE NOVO PROTEIN / beta-hairpin / nanotube assembly
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.082 Å
AuthorsYoo, S. / Kreutzer, A.G. / 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: Chem Sci / Year: 2016
Title: Square channels formed by a peptide derived from transthyretin.
Authors: Yoo, S. / Kreutzer, A.G. / Truex, N.L. / Nowick, J.S.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence
Category: pdbx_audit_support / pdbx_validate_polymer_linkage
Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORN-THR-ILE-ALA-MAA-LEU-LEU-SER-ORN-SER-PHI-SER-THR-THR-ALA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,7852
Polymers1,7501
Non-polymers351
Water25214
1
A: ORN-THR-ILE-ALA-MAA-LEU-LEU-SER-ORN-SER-PHI-SER-THR-THR-ALA-VAL
hetero molecules

A: ORN-THR-ILE-ALA-MAA-LEU-LEU-SER-ORN-SER-PHI-SER-THR-THR-ALA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5704
Polymers3,5002
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area410 Å2
ΔGint-12 kcal/mol
Surface area3210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.300, 42.300, 16.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-101-

CL

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Components

#1: Protein/peptide ORN-THR-ILE-ALA-MAA-LEU-LEU-SER-ORN-SER-PHI-SER-THR-THR-ALA-VAL


Mass: 1749.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.3 % / Description: Thin elongated rods
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1 M NaOAc pH 5.3, 0.2 M CaCl2, and 31% isopropanol

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Aug 29, 2015
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.082→21.15 Å / Num. obs: 2053 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.04945 / Net I/av σ(I): 13.92 / Net I/σ(I): 13.92
Reflection shellResolution: 2.082→2.157 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1101 / Mean I/σ(I) obs: 5.49 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: 000)refinement
MOSFLM7.2.1data reduction
Aimless0.5.17data scaling
PHASER(1.10.1_2155: 000)phasing
RefinementMethod to determine structure: SAD / Resolution: 2.082→21.15 Å / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 10.23
RfactorNum. reflection% reflection
Rfree0.1839 172 10.12 %
Rwork0.1593 --
obs0.162 1700 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.082→21.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms114 0 1 14 129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006115
X-RAY DIFFRACTIONf_angle_d0.971155
X-RAY DIFFRACTIONf_dihedral_angle_d27.28178
X-RAY DIFFRACTIONf_chiral_restr0.04723
X-RAY DIFFRACTIONf_plane_restr0.00417
LS refinement shellResolution: 2.0818→21.15 Å
RfactorNum. reflection% reflection
Rfree0.1839 172 -
Rwork0.1593 1528 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 33.2569 Å / Origin y: 26.7672 Å / Origin z: 7.6429 Å
111213212223313233
T0.1397 Å2-0.0016 Å2-0.0195 Å2-0.0909 Å20.0166 Å2--0.1328 Å2
L0.6076 °20.7292 °2-1.2306 °2-2.3002 °2-2.5154 °2--3.7037 °2
S-0.0806 Å °0.0185 Å °-0.0986 Å °0.1317 Å °0.1887 Å °0.1426 Å °0.2714 Å °-0.1213 Å °-0.056 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 2 through 16 )

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