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- PDB-4p4v: Hexamer formed by a macrocyclic peptide derived from beta-2-micro... -

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Basic information

Entry
Database: PDB / ID: 4p4v
TitleHexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVA(MAA)AVK
ComponentsCYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVA(MAA)AVK
KeywordsDE NOVO PROTEIN / Hexamer / beta-2 microglobulin / amyloid / iodophenylalanine
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.97 Å
AuthorsSpencer, R.K. / 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 / Category: pdbx_audit_support / 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)KVA(MAA)AVK
B: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVA(MAA)AVK
C: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVA(MAA)AVK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3539
Polymers5,9583
Non-polymers3956
Water27015
1
A: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVA(MAA)AVK
B: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVA(MAA)AVK
C: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVA(MAA)AVK
hetero molecules

A: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVA(MAA)AVK
B: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVA(MAA)AVK
C: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVA(MAA)AVK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,70618
Polymers11,9176
Non-polymers78912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area6900 Å2
ΔGint-135 kcal/mol
Surface area6520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.030, 62.030, 44.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein/peptide CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVA(MAA)AVK


Mass: 1986.140 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.61 Å3/Da / Density % sol: 65.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris, pH 8.0; 0.3 M lithium sulfate; 45% PEG 400
PH range: 7.0-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 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: 1.97→31.3 Å / Num. obs: 6556 / % possible obs: 99.88 % / Redundancy: 2 % / Rmerge(I) obs: 0.03705 / Net I/σ(I): 13.24
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3766 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.97→31.299 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 1192 10.15 %
Rwork0.1946 --
obs0.1975 11748 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→31.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms396 0 18 15 429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008472
X-RAY DIFFRACTIONf_angle_d1.276642
X-RAY DIFFRACTIONf_dihedral_angle_d30.442221
X-RAY DIFFRACTIONf_chiral_restr0.05871
X-RAY DIFFRACTIONf_plane_restr0.00572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.05010.32371330.29511176X-RAY DIFFRACTION99
2.0501-2.14340.3671300.30921175X-RAY DIFFRACTION100
2.1434-2.25630.28011370.26181159X-RAY DIFFRACTION100
2.2563-2.39770.20921260.20431188X-RAY DIFFRACTION100
2.3977-2.58270.21171330.2081177X-RAY DIFFRACTION100
2.5827-2.84250.25341390.21041158X-RAY DIFFRACTION100
2.8425-3.25340.18551290.16591173X-RAY DIFFRACTION100
3.2534-4.09750.18861310.17961178X-RAY DIFFRACTION99
4.0975-31.30280.22561340.17441172X-RAY DIFFRACTION99
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)
15.4012-1.10891.28999.4804-6.48154.4940.0930.0358-0.1207-0.4633-0.0877-0.12950.42220.1154-0.04010.31080.0350.04520.3045-0.00530.3271-23.7914-13.62655.1765
25.16555.3246-3.06525.5785-3.71327.0760.0813-0.41760.2814-0.17110.00540.4901-0.4523-0.2566-0.13090.3410.0414-0.0060.2591-0.00390.3986-29.9847-9.06526.3802
33.3849-5.40893.07269.2428-5.13023.0405-0.0961-0.07750.31670.4238-0.09020.0492-0.1557-0.46160.05680.3499-0.00910.03910.3914-0.05130.2298-32.3275-23.19063.8873
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 )

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