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- PDB-4p4z: Octomer formed by a macrocyclic peptide derived from beta-2-micro... -

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Basic information

Entry
Database: PDB / ID: 4p4z
TitleOctomer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
ComponentsCYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
KeywordsDE NOVO PROTEIN / Octamer / beta-sheet / amyloid / beta-2 microglobulin
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.31 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
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 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_symmetry

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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(MVA)TVK
B: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
C: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
D: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
E: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
F: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
G: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
H: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
I: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
J: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
K: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
L: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,43520
Polymers24,89112
Non-polymers5448
Water6,035335
1
A: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
B: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
C: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
D: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)17,21016
Polymers16,5948
Non-polymers6168
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8540 Å2
ΔGint-90 kcal/mol
Surface area6680 Å2
MethodPISA
2
E: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
F: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
G: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
H: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
I: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
J: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
K: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
L: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,83012
Polymers16,5948
Non-polymers2364
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-85 kcal/mol
Surface area6760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.310, 63.310, 126.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 2074.245 Da / Num. of mol.: 12 / Mutation: Y86PHI / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#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 / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10
Details: PEG 1500 35%, 0.1 M SPG buffer (2:7:7 - succinic acid:sodium dihydrogen phosphate:glycine)

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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: Jun 20, 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: 1.31→35.13 Å / Num. obs: 62669 / % possible obs: 99.96 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.0786 / Net I/σ(I): 16.09
Reflection shellResolution: 1.31→1.357 Å / Redundancy: 7 % / Rmerge(I) obs: 1.108 / Mean I/σ(I) obs: 1.76 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.31→35.13 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1745 5909 5 %Phenix-selected
Rwork0.1509 ---
obs0.152 118173 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.31→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 28 335 2019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151874
X-RAY DIFFRACTIONf_angle_d1.6022546
X-RAY DIFFRACTIONf_dihedral_angle_d26.157850
X-RAY DIFFRACTIONf_chiral_restr0.089314
X-RAY DIFFRACTIONf_plane_restr0.009276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.32490.30581970.30683772X-RAY DIFFRACTION100
1.3249-1.34050.31151910.29733678X-RAY DIFFRACTION100
1.3405-1.35680.2872010.27513786X-RAY DIFFRACTION100
1.3568-1.3740.28691970.26043784X-RAY DIFFRACTION100
1.374-1.39210.28831890.25633692X-RAY DIFFRACTION100
1.3921-1.41110.28652020.24763765X-RAY DIFFRACTION100
1.4111-1.43130.2751920.23133720X-RAY DIFFRACTION100
1.4313-1.45270.25511980.22333755X-RAY DIFFRACTION100
1.4527-1.47540.20351930.21353771X-RAY DIFFRACTION100
1.4754-1.49960.20971930.19923688X-RAY DIFFRACTION100
1.4996-1.52540.20961970.19733749X-RAY DIFFRACTION100
1.5254-1.55320.20541970.18353776X-RAY DIFFRACTION100
1.5532-1.5830.18142040.17723795X-RAY DIFFRACTION100
1.583-1.61530.20651990.17753720X-RAY DIFFRACTION100
1.6153-1.65050.20961950.17513703X-RAY DIFFRACTION100
1.6505-1.68890.17141980.16523746X-RAY DIFFRACTION100
1.6889-1.73110.17032000.15263746X-RAY DIFFRACTION100
1.7311-1.77790.20972000.15083733X-RAY DIFFRACTION100
1.7779-1.83020.16381960.14053729X-RAY DIFFRACTION100
1.8302-1.88930.15542020.13183777X-RAY DIFFRACTION100
1.8893-1.95680.18882000.13633715X-RAY DIFFRACTION100
1.9568-2.03510.15491930.13853765X-RAY DIFFRACTION100
2.0351-2.12780.14061950.11563728X-RAY DIFFRACTION100
2.1278-2.23990.13781950.12153774X-RAY DIFFRACTION100
2.2399-2.38020.11771940.11473723X-RAY DIFFRACTION100
2.3802-2.5640.1661960.13013784X-RAY DIFFRACTION100
2.564-2.82190.14631970.13013723X-RAY DIFFRACTION100
2.8219-3.230.18751970.133739X-RAY DIFFRACTION100
3.23-4.06840.15971980.12393716X-RAY DIFFRACTION100
4.0684-35.1480.14232030.13823712X-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)
14.1753-3.11623.43655.0547-3.90173.66420.0771-0.0077-0.0128-0.00890.0429-0.1438-0.00070.1461-0.12450.0962-0.02690.01190.1-0.01130.1222-8.21233.86344.1006
26.73284.3819-5.38383.09-4.27026.97430.1591-0.07830.158-0.049-0.0180.13530.08930.0827-0.15460.11320.03120.00190.0901-0.00730.12153.185811.13184.1914
37.8026-5.9943-5.17144.9855.05566.51680.27620.32960.0545-0.0803-0.1547-0.0992-0.112-0.1682-0.11580.0906-0.03740.00310.09260.010.1279-0.09610.4634-5.7389
45.23232.7302-2.90766.1457-2.89066.6901-0.0230.07450.2591-0.17740.1392-0.077-0.24260.1069-0.08370.09780.01410.00080.0816-0.00760.1037-7.2334-0.5724-5.4265
55.39934.9906-5.39755.8132-4.71196.9422-0.144-0.0419-0.003-0.0801-0.0738-0.10240.19220.0230.21590.0730.0008-0.0260.1077-0.01380.0859-20.6814-5.3417-1.484
65.009-1.54162.17494.588-1.32397.5956-0.00230.15020.1543-0.1945-0.06030.0499-0.06820.07840.07830.06920.00170.02450.08140.00590.0911-21.09144.91591.2219
75.60361.27141.54086.2581.45295.2190.01760.0433-0.2031-0.09240.03130.07760.1641-0.1109-0.05440.05860.0050.02080.08190.00610.0766-29.0049-5.28889.3841
85.75023.8727-4.88237.3351-5.18365.27580.2212-0.00840.22830.1668-0.07860.0624-0.15310.0763-0.15060.07770.0136-0.02920.1027-0.00880.0883-32.74694.42099.2189
94.8927-2.2861-3.10755.5024.43237.6433-0.13010.2347-0.2559-0.0816-0.17330.21610.3272-0.02690.26260.10370.0062-0.01670.10790.0010.0887-39.7153-5.80021.2151
104.71662.13162.66983.92010.03785.763-0.0471-0.13290.11030.334-0.0289-0.0021-0.02030.00620.11080.07880.01120.02450.0984-0.01440.098-39.17914.8879-1.4216
117.4385-5.5758-3.60954.32842.95022.45430.127-0.05850.07240.176-0.1504-0.06810.0424-0.0626-0.05920.1067-0.0137-0.02210.1095-0.00140.0826-27.27793.4113-9.7139
126.4506-5.47775.52528.7298-5.23384.97170.2387-0.0584-0.1342-0.2084-0.1055-0.05920.21780.0907-0.14440.0796-0.00620.03360.1098-0.00460.084-31.4831-5.5567-9.2077
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
8X-RAY DIFFRACTION8chain 'H' and ( resid 1 through 16 )H1 - 16
9X-RAY DIFFRACTION9chain 'I' and ( resid 1 through 16 )I1 - 16
10X-RAY DIFFRACTION10chain 'J' and ( resid 1 through 16 )J1 - 16
11X-RAY DIFFRACTION11chain 'K' and ( resid 1 through 16 )K1 - 16
12X-RAY DIFFRACTION12chain 'L' and ( resid 1 through 16 )L1 - 16

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