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- PDB-6eex: L-GSTSTA from degenerate octameric repeats in InaZ, residues 707-712 -

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Basic information

Entry
Database: PDB / ID: 6eex
TitleL-GSTSTA from degenerate octameric repeats in InaZ, residues 707-712
ComponentsL-GSTSTA from ice nucleaction protein, inaZ
KeywordsPROTEIN FIBRIL / amyloid / racemic / ice nucleation / MicroED / InaZ / pseudomonas syringae
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å
AuthorsZee, C. / Glynn, C. / Gallagher-Jones, M. / Miao, J. / Santiago, C.G. / Cascio, D. / Gonen, T. / Sawaya, M.R. / Rodriguez, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
CitationJournal: IUCrJ / Year: 2019
Title: Homochiral and racemic MicroED structures of a peptide repeat from the ice-nucleation protein InaZ.
Authors: Chih-Te Zee / Calina Glynn / Marcus Gallagher-Jones / Jennifer Miao / Carlos G Santiago / Duilio Cascio / Tamir Gonen / Michael R Sawaya / Jose A Rodriguez /
Abstract: The ice-nucleation protein InaZ from contains a large number of degenerate repeats that span more than a quarter of its sequence and include the segment GSTSTA. structures of this repeat segment, ...The ice-nucleation protein InaZ from contains a large number of degenerate repeats that span more than a quarter of its sequence and include the segment GSTSTA. structures of this repeat segment, resolved to 1.1 Å by microfocus X-ray crystallography and to 0.9 Å by the cryo-EM method MicroED, were determined from both racemic and homochiral crystals. The benefits of racemic protein crystals for structure determination by MicroED were evaluated and it was confirmed that the phase restriction introduced by crystal centrosymmetry increases the number of successful trials during the phasing of the electron diffraction data. Both homochiral and racemic GSTSTA form amyloid-like protofibrils with labile, corrugated antiparallel β-sheets that mate face to back. The racemic GSTSTA protofibril represents a new class of amyloid assembly in which all-left-handed sheets mate with their all-right-handed counterparts. This determination of racemic amyloid assemblies by MicroED reveals complex amyloid architectures and illustrates the racemic advantage in macromolecular crystallography, now with submicrometre-sized crystals.
History
DepositionAug 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-GSTSTA from ice nucleaction protein, inaZ


Theoretical massNumber of molelcules
Total (without water)5231
Polymers5231
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)9.210, 11.980, 22.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide L-GSTSTA from ice nucleaction protein, inaZ


Mass: 522.508 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide L-GSTSTA corresponding to segment 707-712 of InaZ
Source: (synth.) Pseudomonas syringae (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.1M CHES pH 9.5, 10% (w/v) of PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.1→11.4 Å / Num. obs: 1093 / % possible obs: 91.7 % / Redundancy: 6.476 % / Biso Wilson estimate: 3.4 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.136 / Χ2: 0.964 / Net I/σ(I): 10.41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.156.4270.2197.341170.9790.24374.5
1.15-1.226.2990.237.51370.9730.24998.6
1.22-1.296.8870.1968.271150.9910.21285.2
1.29-1.386.770.199.351260.9730.20694.7
1.38-1.496.7740.1759.181150.9840.18995
1.49-1.636.7450.14111.42980.9920.15292.5
1.63-1.826.5480.13311.381040.9850.14595.4
1.82-2.116.7030.10513.93910.9880.11397.8
2.11-2.586.0860.08914.33810.9950.09796.4
2.58-3.655.9060.08115.5640.9790.09294.1
3.65-11.44.80.06613.01450.9990.07595.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→11.4 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 5
RfactorNum. reflection% reflection
Rfree0.0688 107 9.95 %
Rwork0.0613 --
obs0.0622 1075 91.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 4.78 Å2 / Biso mean: 2.0668 Å2 / Biso min: 1.01 Å2
Refinement stepCycle: final / Resolution: 1.1→11.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36 0 0 1 37
Biso mean---4.78 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00735
X-RAY DIFFRACTIONf_angle_d1.54747
X-RAY DIFFRACTIONf_chiral_restr0.0727
X-RAY DIFFRACTIONf_plane_restr0.0066
X-RAY DIFFRACTIONf_dihedral_angle_d9.2610
LS refinement shellResolution: 1.1001→1.1501 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.0795 11 9 %
Rwork0.0721 968 -
obs-97 74 %

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