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- PDB-2omp: LYQLEN peptide derived from human insulin chain A, residues 13-18 -

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Basic information

Entry
Database: PDB / ID: 2omp
TitleLYQLEN peptide derived from human insulin chain A, residues 13-18
ComponentsLYQLEN peptide derived from human insulin chain A, residues 13-18
KeywordsPROTEIN FIBRIL / steric zipper / antiparallel beta-sheet
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsIvanova, M.I. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Nature / Year: 2007
Title: Atomic structures of amyloid cross-beta spines reveal varied steric zippers.
Authors: Sawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M.I. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H.T. / Madsen, A.O. / Riekel, C. / Eisenberg, D.
History
DepositionJan 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYQLEN peptide derived from human insulin chain A, residues 13-18
B: LYQLEN peptide derived from human insulin chain A, residues 13-18


Theoretical massNumber of molelcules
Total (without water)1,5582
Polymers1,5582
Non-polymers00
Water1086
1
A: LYQLEN peptide derived from human insulin chain A, residues 13-18
B: LYQLEN peptide derived from human insulin chain A, residues 13-18

A: LYQLEN peptide derived from human insulin chain A, residues 13-18
B: LYQLEN peptide derived from human insulin chain A, residues 13-18

A: LYQLEN peptide derived from human insulin chain A, residues 13-18
B: LYQLEN peptide derived from human insulin chain A, residues 13-18

A: LYQLEN peptide derived from human insulin chain A, residues 13-18
B: LYQLEN peptide derived from human insulin chain A, residues 13-18


Theoretical massNumber of molelcules
Total (without water)6,2318
Polymers6,2318
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_656x+1,y,z+11
Unit cell
Length a, b, c (Å)9.666, 28.003, 17.346
Angle α, β, γ (deg.)90.000, 96.240, 90.000
Int Tables number4
Space group name H-MP1211
DetailsOne sheet of the steric zipper can be generated by repeated application of the crystallographic unit cell translation along the a axis. The second sheet of the steric zipper can be generated by application of the crystallographic operator X,Y,Z+1, and repeated unit cell translations of this strand along the a axis.

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Components

#1: Protein/peptide LYQLEN peptide derived from human insulin chain A, residues 13-18


Mass: 778.850 Da / Num. of mol.: 2 / Fragment: residues 13-18 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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

Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 2.5
Details: 20mM peptide in 100 mM NaCl and 50 mM phosphate, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9466
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9466 Å / Relative weight: 1
ReflectionResolution: 1.8→90 Å / Num. obs: 752 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.186 / Χ2: 1.11 / Net I/σ(I): 4.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.941.90.4021371.051183.5
1.94-2.1320.281421.079189.3
2.13-2.4420.2631541.07190.1
2.44-3.082.20.1831591.122197
3.08-902.30.131601.185195.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: idealized beta strands, polyalanine

Resolution: 1.9→17.24 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.81 / SU B: 9.051 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 41 6 %RANDOM
Rwork0.189 ---
obs0.191 682 91.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.283 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.29 Å2
2---0.06 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms110 0 0 6 116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022113
X-RAY DIFFRACTIONr_bond_other_d0.0120.02103
X-RAY DIFFRACTIONr_angle_refined_deg1.3572.072152
X-RAY DIFFRACTIONr_angle_other_deg2.0153241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.755510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.74327.58
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.2231522
X-RAY DIFFRACTIONr_chiral_restr0.0410.217
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0218
X-RAY DIFFRACTIONr_nbd_refined0.190.211
X-RAY DIFFRACTIONr_nbd_other0.2010.262
X-RAY DIFFRACTIONr_nbtor_refined0.1940.235
X-RAY DIFFRACTIONr_nbtor_other0.090.270
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.24
X-RAY DIFFRACTIONr_mcbond_it3.2371.591
X-RAY DIFFRACTIONr_mcbond_other0.0451.528
X-RAY DIFFRACTIONr_mcangle_it2.389295
X-RAY DIFFRACTIONr_scbond_it5.139369
X-RAY DIFFRACTIONr_scangle_it5.4654.557
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 4 -
Rwork0.311 38 -
obs-42 75 %
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)
10.36191.5235-1.11327.065-5.0593.6373-0.1074-0.0113-0.0316-0.02290.1190.0018-0.084-0.0397-0.01160.00540.0084-0.01630.01370.0251-0.02491.13961.9733-0.9879
20.69132.1575-1.7466.7672-5.43384.41720.0682-0.016-0.07850.01740.08250.1744-0.072-0.1234-0.1507-0.02980.00610.00530.00190.01740.00366.10022.2679-0.4459
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 6 / Label seq-ID: 1 - 6

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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