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- PDB-6mxf: MicroED structure of thiostrepton at 1.9 A resolution -

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Basic information

Entry
Database: PDB / ID: 6mxf
TitleMicroED structure of thiostrepton at 1.9 A resolution
ComponentsThiostrepton
KeywordsANTIBIOTIC
Function / homologyThiazolylpeptide-type bacteriocin precursor / defense response to bacterium / extracellular region / Thiostrepton
Function and homology information
Specimen sourceStreptomyces azureus (bacteria)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / 1.91 Å resolution
AuthorsJones, C.G. / Martynowycz, M.W. / Hattne, J. / Fulton, T. / Stoltz, B.M. / Rodriguez, J.A. / Nelson, H.M. / Gonen, T.
CitationJournal: Acs Cent.Sci. / Year: 2018
Title: The CryoEM Method MicroED as a Powerful Tool for Small Molecule Structure Determination
Authors: Jones, C.G. / Martynowycz, M.W. / Hattne, J. / Fulton, T. / Stoltz, B.M. / Rodriguez, J.A. / Nelson, H.M. / Gonen, T.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 30, 2018 / Release: Nov 21, 2018

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Structure visualization

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Assembly

Deposited unit
A: Thiostrepton


Theoretical massNumber of molelcules
Total (without water)1,8061
Polyers1,8061
Non-polymers00
Water362
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)400
ΔGint (kcal/M)1
Surface area (Å2)1690
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)26.219, 26.219, 27.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP 43 21 2

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Components

#1: Protein/peptide Thiostrepton /


Mass: 1805.985 Da / Num. of mol.: 1
Feature: PRD_000223
classAntibiotic
detailsThiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain residue 1 and side-chain of residue 12. Post translational maturation of thiazole and oxazole containing antibiotics involves the enzymic condensation of a Cys or Ser with the alpha-carbonyl of the preceding amino acid to form a thioether or ether bond, then dehydration to form a double bond with the alpha-amino nitrogen. Thiazoline or oxazoline ring are dehydrogenated to form thiazole or oxazole rings. the pyridinyl involves the cross-linking of a Ser and a Cys-Ser pair usually separated by 7 or 8 residues along the peptide chain. The Ser residues are dehydrated to didehydroalanines, then bonded between their beta carbons. The alpha carbonyl of the Cys condenses with alpha carbon of the first Ser to form a pyridinyl ring. The ring may be mutiply dehydrogenated to form a pyridine ring with loss of the amino nitrogen of the first Ser. The amidation of Ser-17 probably does not occur by the same mechanism, oxidative cleavage of glycine, as in eukaryotes.
nameTHIOSTREPTON
typeThiopeptide

Source: (synth.) Streptomyces azureus (bacteria) / References: UniProt: P0C8P8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Formula: H2O / Water
Compound detailsTHIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC ...THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC CORE, CONSISTING OF A NITROGEN CONTAINING, SIX-MEMBERED RING CENTRAL TO DEHYDROAMINO ACIDS AND A SUBSET OF FIVE MEMBER RING STRUCTURES INCLUDING THIAZOLES, THIAZOLINES AND OXAZOLES. HERE, THIOSTREPTON IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / Reconstruction method: electron crystallography

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Sample preparation

ComponentName: Thiostrepton / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: NATURAL
Molecular weightValue: .001619538000 MDa / Experimental value: NO
Source (natural)Organism: Streptomyces azureus (bacteria)
EM crystal formationDetails: Powder
Buffer solutionDetails: Powder / pH: 7
SpecimenDetails: Powder / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R2/2
VitrificationCryogen name: NITROGEN / Humidity: 100 % / Chamber temperature: 298 kelvins / Details: Hand-plunged

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Data collection

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.21 sec. / Electron dose: 0.09 e/Å2 / Details: FEI CetaD / Film or detector model: FEI CETA (4k x 4k) / Number of diffraction images: 214 / Number of grids imaged: 1
Image scansSampling size: 28 microns / Width: 2048 / Height: 2048
EM diffractionCamera length: 960 mm
EM diffraction shellFourier space coverage: 40.3 / High resolution: 1.91 Å / Low resolution: 2.13 Å / Multiplicity: 4.9 / Number of structure factors: 92 / Phase residual: 29.19 deg.
EM diffraction statsFourier space coverage: 78.6 / High resolution: 1.91 Å / Number of intensities measured: 5578 / Number of structure factors: 686 / Overall phase error: 26.93 deg. / Overall phase residual: 26.93 deg. / Phase error rejection criteria: 0 / R merge: 0.236 / R sym: 0.236
DetectorCollection date: Oct 3, 2018
ReflectionD resolution high: 1.9 Å / D resolution low: 18.99 Å / Number obs: 686 / CC half: 0.985 / Rmerge I obs: 0.236 / Rpim I all: 0.084 / Rrim I all: 0.251 / NetI over sigmaI: 5.1 / Redundancy: 8.1 % / Percent possible obs: 78.6
Reflection shellRmerge I obs: 0.32 / Highest resolution: 1.9 Å / Lowest resolution: 2.13 Å / MeanI over sigI obs: 3.4 / Number unique all: 93 / CC half: 0.813 / Redundancy: 4.9 % / Percent possible all: 40.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLM7.2.2data reduction
Aimless0.7.3data scaling
MOLREP11.6.04phasing
EM software
IDNameVersionCategory
6MOLREP11.6.04model fitting
8MOLREP11.6.04molecular replacement
10POINTLESS1.11.14symmetry determination
11AIMLESS0.7.3crystallography merging
13REFMAC5.8.0232model refinement
Image processingDetails: FEI Ceta
EM 3D crystal entityAngle alpha: 90 deg. / Angle beta: 90 deg. / Angle gamma: 90 deg. / Length a: 26.219 Å / Length b: 26.219 Å / Length c: 27.534 Å / Space group name: P 43 21 2 / Space group num: 96
CTF correctionType: NONE
3D reconstructionResolution: 1.91 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingOverall b value: 2.6 / Ref protocol: OTHER / Ref space: RECIPROCAL
Atomic model buildingPDB-ID: 1E9W
Pdb chain ID: A / Pdb chain residue range: 0-18
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1e9w
Correlation coeff Fo to Fc: 0.931 / Correlation coeff Fo to Fc free: 0.94 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 3.282 / Overall SU ML: 0.098 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Overall ESU R: 0.352 / Overall ESU R Free: 0.202
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å
Displacement parametersB iso mean: 6.811 Å2 / Aniso B11: 0.18 Å2 / Aniso B12: - Å2 / Aniso B13: - Å2 / Aniso B22: 0.18 Å2 / Aniso B23: - Å2 / Aniso B33: -0.37 Å2
Least-squares processR factor R free: 0.21798 / R factor R work: 0.19046 / R factor obs: 0.19276 / Highest resolution: 1.91 Å / Lowest resolution: 18.99 Å / Number reflection R free: 57 / Number reflection obs: 620 / Percent reflection R free: 8.4 / Percent reflection obs: 78.18
Number of atoms included #1Total: 116
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0150.017123
ELECTRON CRYSTALLOGRAPHYr_bond_other_d0.0250.018107
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg2.7602.241120
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg1.3742.283213
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg3.6235.0003
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg7.90115.0004
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_4_deg
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0620.20015
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0100.020135
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other0.0030.02049
ELECTRON CRYSTALLOGRAPHYr_nbd_refined
ELECTRON CRYSTALLOGRAPHYr_nbd_other
ELECTRON CRYSTALLOGRAPHYr_nbtor_refined
ELECTRON CRYSTALLOGRAPHYr_nbtor_other
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_refined
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_other
ELECTRON CRYSTALLOGRAPHYr_metal_ion_refined
ELECTRON CRYSTALLOGRAPHYr_metal_ion_other
ELECTRON CRYSTALLOGRAPHYr_symmetry_vdw_refined
ELECTRON CRYSTALLOGRAPHYr_symmetry_vdw_other
ELECTRON CRYSTALLOGRAPHYr_symmetry_hbond_refined
ELECTRON CRYSTALLOGRAPHYr_symmetry_hbond_other
ELECTRON CRYSTALLOGRAPHYr_symmetry_metal_ion_refined
ELECTRON CRYSTALLOGRAPHYr_symmetry_metal_ion_other
ELECTRON CRYSTALLOGRAPHYr_mcbond_it0.6250.79862
ELECTRON CRYSTALLOGRAPHYr_mcbond_other0.6200.81063
ELECTRON CRYSTALLOGRAPHYr_mcangle_it0.8931.19437
ELECTRON CRYSTALLOGRAPHYr_mcangle_other0.8811.22338
ELECTRON CRYSTALLOGRAPHYr_scbond_it0.6090.74360
ELECTRON CRYSTALLOGRAPHYr_scbond_other0.6040.75461
ELECTRON CRYSTALLOGRAPHYr_scangle_it
ELECTRON CRYSTALLOGRAPHYr_scangle_other0.8921.16184
ELECTRON CRYSTALLOGRAPHYr_long_range_B_refined1.54610.960101
ELECTRON CRYSTALLOGRAPHYr_long_range_B_other1.53910.959102
ELECTRON CRYSTALLOGRAPHYr_rigid_bond_restr
ELECTRON CRYSTALLOGRAPHYr_sphericity_free
ELECTRON CRYSTALLOGRAPHYr_sphericity_bonded
Refine LS shellHighest resolution: 1.915 Å / R factor R free: 0 / R factor R work: 0.182 / Lowest resolution: 1.964 Å / Number reflection R free: 0 / Number reflection R work: 2 / Total number of bins used: 20 / Percent reflection obs: 3.33

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