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- PDB-4p4x: Dodecamer formed by a macrocyclic peptide derived from beta-2-mic... -

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Basic information

Entry
Database: PDB / ID: 4p4x
TitleDodecamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVA(MLE)AVK
ComponentsCYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK
KeywordsDE NOVO PROTEIN / amyloid / beta-2-microglobulin / macrocycle / dodecamer
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.898 Å
AuthorsSpencer, R.K. / Nowick, J.S.
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 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_validate_polymer_linkage / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _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: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK
B: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK
C: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK
D: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK
E: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK
F: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK
G: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK
H: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK
I: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK
J: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK
K: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK
L: CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,17822
Polymers24,33912
Non-polymers83910
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.343, 61.343, 113.963
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11E-101-

SO4

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Components

#1: Protein/peptide
CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK


Mass: 2028.219 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris, pH 7.5; 0.2 M lithium sulfate; 25% PEG 400

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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: 1.897→32.3 Å / Num. obs: 35831 / % possible obs: 99.91 % / Redundancy: 2 % / Rmerge(I) obs: 0.02883 / Net I/σ(I): 12.49
Reflection shellResolution: 1.897→1.965 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3829 / Mean I/σ(I) obs: 2.02 / % possible all: 99.09

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.898→32.296 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 3284 10.02 %
Rwork0.2087 --
obs0.2115 32770 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.898→32.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 42 70 1732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111688
X-RAY DIFFRACTIONf_angle_d1.4422268
X-RAY DIFFRACTIONf_dihedral_angle_d29.554756
X-RAY DIFFRACTIONf_chiral_restr0.062252
X-RAY DIFFRACTIONf_plane_restr0.007252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.898-1.9260.35471310.32591201X-RAY DIFFRACTION92
1.926-1.95610.31761430.29141301X-RAY DIFFRACTION100
1.9561-1.98820.33091370.28271277X-RAY DIFFRACTION100
1.9882-2.02250.2871460.27861285X-RAY DIFFRACTION100
2.0225-2.05920.28241430.26621279X-RAY DIFFRACTION100
2.0592-2.09880.29481440.23871284X-RAY DIFFRACTION100
2.0988-2.14170.27181430.23411294X-RAY DIFFRACTION100
2.1417-2.18820.25791460.25871283X-RAY DIFFRACTION100
2.1882-2.23910.29881440.24361271X-RAY DIFFRACTION100
2.2391-2.29510.28571400.22911290X-RAY DIFFRACTION100
2.2951-2.35710.25351430.23721300X-RAY DIFFRACTION100
2.3571-2.42650.26621400.22251280X-RAY DIFFRACTION100
2.4265-2.50480.25831380.22441289X-RAY DIFFRACTION100
2.5048-2.59420.25071440.22421290X-RAY DIFFRACTION100
2.5942-2.69810.27021500.24371283X-RAY DIFFRACTION100
2.6981-2.82080.26691470.21271266X-RAY DIFFRACTION100
2.8208-2.96940.25311450.19761295X-RAY DIFFRACTION100
2.9694-3.15530.23041470.19811279X-RAY DIFFRACTION100
3.1553-3.39870.22141460.19691285X-RAY DIFFRACTION100
3.3987-3.74030.22211400.19121283X-RAY DIFFRACTION100
3.7403-4.28040.17551410.17751288X-RAY DIFFRACTION100
4.2804-5.38880.19051400.16421306X-RAY DIFFRACTION100
5.3888-32.30110.21971460.20861277X-RAY DIFFRACTION100
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)
17.4118-5.023-2.57787.1311.13276.8984-0.167-0.46710.65170.6285-0.0604-0.3243-0.12810.11770.31640.305-0.1413-0.10450.37580.08810.14540.376711.81045.181
23.2976-1.32961.13741.1149-1.69143.0917-0.08830.4553-0.4197-0.28890.13340.0780.5343-0.2812-0.82010.2742-0.1229-0.16520.31230.10920.34656.6413.03820.8094
37.71534.95242.23445.22892.62952.5068-0.55380.8788-0.0481-0.45120.4625-0.7848-0.30590.12580.43380.2786-0.0218-0.16860.25830.16510.37288.897523.4813.3956
41.0926-0.84210.38467.1452-2.83284.17980.15510.0458-0.06150.0577-0.3658-1.5818-0.06470.1694-0.55770.2868-0.064-0.20610.17820.06650.258416.926320.43723.1693
53.1198-2.6738-0.29084.50861.11122.6379-0.07180.23830.4572-0.0518-0.1352-1.06810.18970.11980.32160.3484-0.1985-0.07390.36730.10640.19621.9424.22112.3115
66.50211.4043-0.91165.3629-1.33591.73560.21320.14521.4895-0.14420.10641.0031-0.0029-0.48790.02910.3309-0.086-0.17760.22820.32790.069513.502613.09065.134
75.6352.97480.82782.40191.16071.07730.1595-0.66650.35340.9725-0.2742-0.02410.3613-0.28140.69590.3012-0.0799-0.21130.30260.09060.276617.51056.125815.4526
84.3499-1.37613.29433.4655-2.94626.6762-0.20970.11950.7370.57240.35310.2646-0.9242-0.0173-0.03180.1662-0.1557-0.2720.3880.21090.390824.035516.833511.9349
95.1657-2.4333-5.70184.20211.16456.9734-0.06761.0327-0.21710.314-0.3066-0.40910.2037-0.564-0.06080.3624-0.0759-0.22890.21720.00840.424626.317912.235726.6916
107.67310.6759-4.21684.059-0.69026.86670.2122-0.10840.13690.2264-0.00740.0399-0.1695-0.00850.70450.3412-0.0637-0.08640.15180.05650.228118.6595.251128.4879
115.35940.377-2.20076.72520.98017.3766-0.3032-0.068-0.94250.8725-0.0924-0.70230.32060.57330.19390.2965-0.0508-0.0320.38290.32030.434516.746428.28264.1292
126.74861.89320.75582.01492.24645.5912-0.56480.51351.3594-0.6652-0.0686-0.2851-1.3295-0.3239-0.22750.5504-0.2909-0.19140.47390.28781.029623.277830.00313.2225
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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