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- PDB-1e9w: Structure of the macrocycle thiostrepton solved using the anomalo... -

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Basic information

Entry
Database: PDB / ID: 1e9w
TitleStructure of the macrocycle thiostrepton solved using the anomalous dispersive contribution from sulfur
ComponentsTHIOSTREPTON
KeywordsANTIBIOTIC / THIOPEPTIDE / ANTIBACTERIAL / THIAZOLE / THIAZOLINE / OXAZOLE / RIBOSOME / TRANSLATION INHIBITION
Function / homologyThiazolylpeptide-type bacteriocin precursor / defense response to bacterium / extracellular region / THIOSTREPTON / Thiostrepton
Function and homology information
Biological speciesSTREPTOMYCES AZUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsBond, C.S. / Shaw, M.P. / Alphey, M.S. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of the Macrocycle Thiostrepton Solved Using the Anomalous Dispersive Contribution from Sulfur
Authors: Bond, C.S. / Shaw, M.P. / Alphey, M.S. / Hunter, W.N.
History
DepositionOct 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2001Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 2.0Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOSTREPTON


Theoretical massNumber of molelcules
Total (without water)1,8061
Polymers1,8061
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.577, 26.577, 27.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

21A-2002-

HOH

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Components

#1: Protein/peptide THIOSTREPTON / / ALANINAMIDE / BRYAMYCIN / THIACTIN /


Type: Thiopeptide / Class: Antibiotic / Mass: 1805.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CALBIOCHEM / Source: (natural) STREPTOMYCES AZUREUS (bacteria) / References: UniProt: P0C8P8, THIOSTREPTON
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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) GROUP: 1 NAME: THIOSTREPTON CHAIN: A COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 0 TO 18 DESCRIPTION: THIOSTREPTON IS A HETROCYCLIC THIOPEPTIDE, CONSISTING OF FOUR THIAZOLES ONE THIOZOLINE ONE PIPERIDEINE RINGS. A MODIFIED QUINOLINE LINKED TO MAIN-CHAIN RESIDUE 1 AND SIDE-CHAIN OF RESIDUE 12. THE OBSERVED C-TERMINAL AMINO GROUP NH2(18) IS LIKELY TO BE A POST-TRANSLATIONAL DECARBOXYLATED REMNANT OF A SER C-TERMINAL RESIDUE

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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: 1.46 Å3/Da / Density % sol: 14.8 %
Crystal growpH: 7
Details: 1ML 15.38MG/ML THIOSTREPTON IN CHLOROFORM_ISOAMYL ALCOHOL + 100 MICROL GLYCEROL + 200 MICROL ETHANOL. BATCH METHOD, pH 7.00
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-IDDetails
1protein11100mg
2chloroform/isoamyl alcohol116.5ml
3glycerol110.100ml
4ethanol110.200ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.73
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.73 Å / Relative weight: 1
ReflectionResolution: 1.02→50 Å / Num. obs: 5232 / % possible obs: 96.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 33.8
Reflection shellResolution: 1.02→1.04 Å / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 5.4 / % possible all: 74.6
Reflection
*PLUS
Num. measured all: 22556
Reflection shell
*PLUS
% possible obs: 74.6 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEE REFERENCE

Resolution: 1.02→50 Å / Num. parameters: 1057 / Num. restraintsaints: 1023 / Cross valid method: FREE R-VALUE / σ(F): 0
StereochEM target val spec case: RESIDUE 16 RESTRAINED USING GEOMETRY DERIVED FROM CSD (SEE REFERENCE)
Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1423 825 9.8 %RANDOM
all0.1122 8391 --
obs0.1124 -96.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 115.33
Refinement stepCycle: LAST / Resolution: 1.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms114 0 0 4 118
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0.047
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0001
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.051
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.037
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1173 / Rfactor Rwork: 0.1124
Solvent computation
*PLUS
Displacement parameters
*PLUS

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