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- PDB-8u78: Structure of a N-Me-D-Gln4,Lys10-teixobactin analogue -

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Basic information

Entry
Database: PDB / ID: 8u78
TitleStructure of a N-Me-D-Gln4,Lys10-teixobactin analogue
ComponentsN-Methyl-D-Gln4,Lys10-teixobactin
KeywordsANTIBIOTIC / teixobactin / teixobactin analogue
Function / homology: / Chem-PG6
Function and homology information
Biological speciesEleftheria terrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsNowick, J.S. / Yang, H. / Kreutzer, A.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI121548 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI137258 United States
CitationJournal: J.Org.Chem. / Year: 2024
Title: Supramolecular Interactions of Teixobactin Analogues in the Crystal State.
Authors: Yang, H. / Kreutzer, A.G. / Nowick, J.S.
History
DepositionSep 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-Methyl-D-Gln4,Lys10-teixobactin
B: N-Methyl-D-Gln4,Lys10-teixobactin
C: N-Methyl-D-Gln4,Lys10-teixobactin
D: N-Methyl-D-Gln4,Lys10-teixobactin
E: N-Methyl-D-Gln4,Lys10-teixobactin
F: N-Methyl-D-Gln4,Lys10-teixobactin
G: N-Methyl-D-Gln4,Lys10-teixobactin
H: N-Methyl-D-Gln4,Lys10-teixobactin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,75923
Polymers9,9968
Non-polymers76315
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.880, 24.880, 106.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein/peptide
N-Methyl-D-Gln4,Lys10-teixobactin


Type: Peptide-like / Class: Antibiotic / Mass: 1249.520 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Eleftheria terrae (bacteria) / References: BIRD: PRD_002532
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H26O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.65 Å3/Da / Density % sol: 25.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG3350, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 1.5→24.88 Å / Num. obs: 10322 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 14.35 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01774 / Rpim(I) all: 0.01774 / Rrim(I) all: 0.02509 / Net I/σ(I): 24.09
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1934 / Mean I/σ(I) obs: 4.24 / Num. unique obs: 1055 / CC1/2: 0.916 / CC star: 0.978 / Rpim(I) all: 0.1934 / Rrim(I) all: 0.2735 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
BOSB3data collection
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
PHENIXHYSSphasing
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→24.88 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 22.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1831 1030 9.98 %282
Rwork0.1544 ---
obs0.1574 10318 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms696 0 32 74 802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014713
X-RAY DIFFRACTIONf_angle_d2.013944
X-RAY DIFFRACTIONf_dihedral_angle_d31.778122
X-RAY DIFFRACTIONf_chiral_restr0.098128
X-RAY DIFFRACTIONf_plane_restr0.009104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.580.25781480.20741333X-RAY DIFFRACTION100
1.58-1.680.24371470.18131339X-RAY DIFFRACTION100
1.68-1.810.25531460.18571293X-RAY DIFFRACTION100
1.81-1.990.22481430.17281337X-RAY DIFFRACTION100
1.99-2.280.20011420.16721336X-RAY DIFFRACTION100
2.28-2.870.16211560.15621309X-RAY DIFFRACTION100
2.87-24.880.14911480.12661341X-RAY DIFFRACTION100

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