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- PDB-4hp2: Invariom refinement of a new dimeric monoclinic 2 solvate of thio... -

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Entry
Database: PDB / ID: 4hp2
TitleInvariom refinement of a new dimeric monoclinic 2 solvate of thiostrepton at 0.64 angstrom resolution
ComponentsThiostrepton
KeywordsANTIBIOTIC / THIOPEPTIDE / ANTIBACTERIAL / THIAZOLE / THIAZOLINE / OXAZOLE / RIBOSOME / TRANSLATION INHIBITION
Function / homologyThiazolylpeptide-type bacteriocin precursor / defense response to bacterium / extracellular region / THIOSTREPTON / DIMETHYLFORMAMIDE / diethyl ether / Thiostrepton
Function and homology information
Biological speciesStreptomyces azureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SHELXS/DIRECT-METHODS / Resolution: 0.64 Å
AuthorsProepper, K. / Holstein, J.J. / Huebschle, C.B. / Bond, C.S. / Dittrich, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Invariom refinement of a new monoclinic solvate of thiostrepton at 0.64 angstrom resolution.
Authors: Propper, K. / Holstein, J.J. / Hubschle, C.B. / Bond, C.S. / Dittrich, B.
History
DepositionOct 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.detector / _diffrn_detector.type ..._diffrn_detector.detector / _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiostrepton
B: Thiostrepton
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,64116
Polymers3,6122
Non-polymers1,02914
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)21.394, 22.870, 22.780
Angle α, β, γ (deg.)90.00, 106.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Thiostrepton / Alaninamide / Bryamycin / Gargon / Thiactin


Type: Thiopeptide / Class: Antibiotic / Mass: 1805.985 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 56-72 / Source method: isolated from a natural source
Details: Thiostrepton 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 ...Details: Thiostrepton 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.
Source: (natural) Streptomyces azureus (bacteria) / Strain: MST-AS4632 / References: UniProt: P0C8P8, THIOSTREPTON
#2: Chemical
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7NO
#3: Chemical
ChemComp-ETZ / diethyl ether


Mass: 74.122 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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)
Sequence detailsA MODIFIED QUINOLINE QUA LINKED TO THE MAIN-CHAIN OF ILE 2 AND THE SIDE-CHAIN OF THR 13. BB9 14 ...A MODIFIED QUINOLINE QUA LINKED TO THE MAIN-CHAIN OF ILE 2 AND THE SIDE-CHAIN OF THR 13. BB9 14 INCLUDES HYDROGEN ATOM H6, THE DEHYDROPIPERIDINE CORE HYDROGEN POSITION AT THE SIX MEMBER RING SYSTEM AMONG SER 6, BB9 14 AND MH6 15.

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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: 1.48 Å3/Da / Density % sol: 16.88 %
Crystal growMethod: vapor diffusion / pH: 7
Details: DIMETHYLFORMAMID, DIETHYLETHER, pH 7.00, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.65
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 0.64→50 Å / Num. obs: 72903 / % possible obs: 91 % / Redundancy: 3.61 % / Rmerge(I) obs: 0.0505 / Net I/σ(I): 16.88
Reflection shellResolution: 0.64→0.65 Å / Redundancy: 0.67 % / Rmerge(I) obs: 0.1457 / Mean I/σ(I) obs: 3.46 / % possible all: 46.4

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Processing

Software
NameClassification
SHELXLrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SHELXS/DIRECT-METHODS / Resolution: 0.64→50 Å / Cross valid method: LEAST SQUARES / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.0678 --
all0.0756 72903 -
obs0.0678 62211 91 %
Refinement stepCycle: LAST / Resolution: 0.64→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms228 0 70 2 300

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