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- PDB-4p4y: Hexamer formed by a macrocyclic peptide derived from beta-2-micro... -

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Basic information

Entry
Database: PDB / ID: 4p4y
TitleHexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
ComponentsCYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
KeywordsDE NOVO PROTEIN / Hexamer / amyloid / beta-2-microglobulin / macrocycle
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.509 Å
AuthorsSpencer, R.K. / Li, H. / Nowick, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1112188 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: X-ray Crystallographic Structures of Oligomers of Peptides Derived from beta 2-Microglobulin.
Authors: Spencer, R.K. / Kreutzer, A.G. / Salveson, P.J. / Li, H. / Nowick, J.S.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: pdbx_audit_support / pdbx_database_status ...pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_validate_polymer_linkage / pdbx_validate_symm_contact
Item: _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible ..._pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 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 / refine_hist / 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.pdbx_ptnr2_label_alt_id / _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: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
B: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
C: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
D: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
E: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
F: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
G: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,75314
Polymers14,3237
Non-polymers4307
Water1,44180
1
A: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
B: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
C: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
hetero molecules

A: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
B: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
C: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,68214
Polymers12,2776
Non-polymers4058
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area6500 Å2
ΔGint-107 kcal/mol
Surface area5850 Å2
MethodPISA
2
D: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
E: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
F: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
hetero molecules

D: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
E: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
F: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,66110
Polymers12,2776
Non-polymers3844
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_566x-y+2/3,-y+4/3,-z+4/31
Buried area6200 Å2
ΔGint-98 kcal/mol
Surface area6500 Å2
MethodPISA
3
G: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)12,49012
Polymers12,2776
Non-polymers2136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area5730 Å2
ΔGint-70 kcal/mol
Surface area6320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.260, 66.260, 154.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-4-

LEU

21D-4-

LEU

31G-101-

CL

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Components

#1: Protein/peptide
CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK


Mass: 2046.192 Da / Num. of mol.: 7 / Mutation: Y86PHI / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M TRIS buffer, pH 7.5; 0.2 M lithium sulfate; 26% PEG 400
PH range: 7.0-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2014
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: 1.509→33.13 Å / Num. obs: 20672 / % possible obs: 98.72 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.05704 / Net I/σ(I): 18.26
Reflection shellResolution: 1.509→1.563 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.4093 / Mean I/σ(I) obs: 3.17 / % possible all: 95.68

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.509→33.13 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1747 1907 5.01 %
Rwork0.1573 --
obs0.1581 38062 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.509→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 0 19 80 1051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141068
X-RAY DIFFRACTIONf_angle_d1.5311446
X-RAY DIFFRACTIONf_dihedral_angle_d31.469507
X-RAY DIFFRACTIONf_chiral_restr0.082171
X-RAY DIFFRACTIONf_plane_restr0.008158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.509-1.54710.24591360.25432480X-RAY DIFFRACTION93
1.5471-1.58890.2241450.21662708X-RAY DIFFRACTION100
1.5889-1.63560.23291400.20882685X-RAY DIFFRACTION99
1.6356-1.68840.19911420.1912683X-RAY DIFFRACTION99
1.6884-1.74880.17181420.17122644X-RAY DIFFRACTION98
1.7488-1.81880.15921350.15392607X-RAY DIFFRACTION97
1.8188-1.90160.1581380.15142609X-RAY DIFFRACTION96
1.9016-2.00180.1551390.14582616X-RAY DIFFRACTION96
2.0018-2.12720.16281360.15142549X-RAY DIFFRACTION94
2.1272-2.29140.18591310.15152540X-RAY DIFFRACTION94
2.2914-2.52190.18381320.14512527X-RAY DIFFRACTION94
2.5219-2.88670.16341380.15752545X-RAY DIFFRACTION94
2.8867-3.63620.1631290.14152470X-RAY DIFFRACTION92
3.6362-33.1380.18091240.1592492X-RAY DIFFRACTION91
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)
14.3629-4.3514.40795.3305-5.96397.32330.17930.2202-0.3363-0.4635-0.11210.26230.17890.3244-0.13030.1885-0.0362-0.00060.1649-0.00890.181116.376224.843368.4738
23.248-0.6587-0.10179.0933-0.06042.8240.04060.0129-0.0828-0.0325-0.06090.1794-0.0511-0.26910.05230.1671-0.0246-0.01530.20060.03030.20218.550524.904472.447
37.33031.4563-6.03993.0121-1.76055.0390.1535-0.08390.377-0.12640.11490.1228-0.37010.0907-0.26660.2304-0.0159-0.0460.19320.01750.185516.939336.308375.4892
45.6363-1.85824.65753.8927-3.11287.90870.1557-0.0404-0.3229-0.02980.13170.26140.3622-0.4409-0.35020.2443-0.04020.00560.15650.00080.162522.113934.387101.8267
57.73893.8212.83427.6112.44095.64980.02840.55090.125-0.58630.233-0.6934-0.39270.5289-0.20890.2269-0.01010.05050.18670.03760.163932.510937.933894.5649
66.39160.4767-4.19875.0696-0.06232.78960.2372-0.68340.370.53590.1114-1.1156-0.20580.4376-0.16010.2776-0.0138-0.07880.2419-0.04580.290136.102844.4071106.7579
77.1634.8883.20317.52045.10133.464-0.16110.20930.6525-0.3719-0.14560.3133-0.3804-0.03740.27270.16660.0042-0.0020.1670.03410.2163-1.83938.590674.2641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ( resid 1 through 16 )A1 - 16
2X-RAY DIFFRACTION2chain 'B' and ( resid 1 through 16 )B1 - 16
3X-RAY DIFFRACTION3chain 'C' and ( resid 1 through 16 )C1 - 16
4X-RAY DIFFRACTION4chain 'D' and ( resid 1 through 16 )D1 - 16
5X-RAY DIFFRACTION5chain 'E' and ( resid 1 through 16 )E1 - 16
6X-RAY DIFFRACTION6chain 'F' and ( resid 1 through 16 )F1 - 16
7X-RAY DIFFRACTION7chain 'G' and ( resid 1 through 16 )G1 - 16

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